How to Do Payroll With Paychex

Payroll services have come a long way in the past few decades, with businesses and employees alike relying on them to make sure everything is handled properly. One company that has been delivering these services for over 30 years is Paychex – one of the largest providers in North America. Here’s what you need to know about how their service works, so you can decide whether or not it might be worth your time to try out.

Paychex is a cloud-based payroll and HR platform that uses Paychex Flex software to assist organizations to manage human resources, benefits, and payroll. You’ll need to consider if you’re small enough to utilize its Paychex Go plan or whether a more premium Paychex Flex plan would work better before signing up for its payroll and HR services. Paychex Go is meant for small enterprises with up to ten workers, while Paychex Flex is for organizations with ten to 49 employees.

New customers engage with an implementation team to set up the program, which integrates all of the company’s current employee and payroll data, making it simple to get started. Payroll processing with Paychex is extremely straightforward: just complete data for a pay period, verify relevant reports and submit. Paychex takes care of the processing and keeps you updated along the route.

Paychex Setup Instructions

1. Enroll in Paychex Go.

You can sign up for Paychex Go in minutes if you need to get up and running fast and don’t require the personal assistance that comes with the higher Paychex Flex plan levels. Simply go to the Paychex website and look at the side-by-side comparisons of the various options. Select the “Sign up Online” option from the Paychex Go menu. You’ll need to submit your name and contact information (email, phone number) and then wait for an email with a sign-up link to arrive; this normally takes seconds.

2. Create a Paychex Go account username and password.

After clicking the link, you’ll be directed to a website where you’ll be asked to create a username and password. When you’re finished, click “Continue.” You’ll see a page with three steps describing how to get started: Provide information about the company and its employees. Run Payroll, and sign paperwork. Choose whether you’ll be processing payroll for a company or for a home (for example, if you’re paying a nanny).

3. Answer a few questions

Paychex needs to make sure the year-to-date payroll data it presents are correct, so you’ll notify the system whether you’ve paid any workers this year. You’ll also be asked how many workers you have.

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Your dashboard is simple to use and organized like a checklist, so you always know what tasks you have left to do.

You should notice a green circle with a white checkmark beside the “About You” section when your dashboard loads. This indicates that the information you supplied about yourself has already been sent, allowing you to begin inputting business information. When you’re finished, go to the bottom of the screen and select “Fix Issues,” and the system will show you all of the items you’re responsible for that require attention.

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As you move through each payroll entry page, you’ll find that certain information, such as a response to the question “Have you paid anybody this year?” is already filled in. Other parts will be left empty. Correct any inaccuracies and enter the data as accurately as possible.

Paychex provides you the option of entering personnel immediately or later. If you want to input them now, make sure you have the essential information, such as their names, pay rates, and benefit deductions.

When you’re asked for your federal employment identification number, click the “Verify” option to have Paychex verify that it’s valid. If you’re depending on memory and don’t have your federal tax ID# available, this is useful.

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The system will alert you if you input an invalid federal EIN#.

The technology may also tell you whether the state you’re in has an income tax. It bases its choice on the address you provide when you register for the service.

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Paychex will notify you whether you are liable for paying state and/or municipal taxes.

The routing and account numbers for your bank account will be entered next. Paychex will withdraw monies to meet your payroll from this account. Then choose “Finish.”

How to Run Payroll with a Paychex Premium Plan

1. Request a Premium Plan Quote.

If you choose a premium plan, such as Paychex Flex Select, you must choose “Get a Quote” beneath the solution you want. For its premium programs, the firm does not advertise prices and instead depends on a unique quotation procedure.

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Paychex is a service that you may join up for. For a Paychex Flex plan, go online or get a quotation.

You’ll be asked for information about your business, such as its name and size. After that, click “Next” and fill in your personal contact information, as well as if you want to be contacted through SMS. You may also get in touch with a member of the sales team via phone or email.

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Paychex’s quotation request form, as shown on a computer screen.

Following the submission of the required information, a sales engineer will contact you to discuss your company’s requirements; you will also be able to book a demo to see how the platform operates. Use the live chat function on the Paychex site if you have any preliminary queries and aren’t ready for a quotation yet.

2. Create an account and collaborate with your implementation team

You’ll have the option to examine the pricing quotation, ask questions, and sign up after being contacted by a Paychex sales representative. After that, you’ll be allocated to an implementation team that will assist you in setting up your account, including providing information about your company and human resources staff. The Paychex implementation team also assists new customers with importing all of their current personnel, year-to-date payroll data, and any other existing HR information.

You’ll be assigned to a customer support specialist after processing a few payrolls with Paychex and working with the installation team. In the Assigned Specialist tile on the user dashboard, you can see your specialist’s contact details. Users may also call the Paychex helpline 24 hours a day, 7 days a week, or visit the website’s frequently asked questions section.

3. Individualize the user’s dashboard and preferences

Take some time to customize the user dashboard based on the features you use the most if you haven’t already. Paychex has a lot of features, like employee benefits administration, time and attendance, and recruiting and onboarding, in addition to payroll, so it’s crucial to have quick access to your preferred tools.

Customize your dashboard by clicking on “Manage Tiles” in the upper right portion of the dashboard and select which tools you’d like front and center. You can also arrange tiles in the order that works best for you. Tiles you may want to prioritize as a payroll administrator include Current Payroll, Last Payroll, Tasks, and Analytics & Reports. The Assigned Specialist tile also makes it easy to get in touch for one-on-one support.

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The Paychex Flex user dashboard is seen in this screenshot.

As an administrator, go to your profile picture in the top right corner of the page and make changes to your user settings, such as updating your profile photo. Changes to business information and settings may also be made by selecting “Company Settings” from the left-hand menu.

4. Assign Access to Users

You may designate user roles to control what each employee can access and update inside the Paychex ecosystem, in addition to configuring your own administrator dashboard. This part of the user customization is usually done during the implementation phase, but it may be changed at any time through the user dashboard.

These options may be found under the “User Access” tab on the left-hand menu. Simply navigate through workers in the user access grid and give particular responsibilities to appropriate parties, such as Payroll Admin or Super Admin.

5. Customize Analytics and Reporting

Paychex Flex, like user preferences, allows administrators to pick whatever reports and analytic tools they want to employ in their HR and payroll processes. Paychex offers over 160 basic dashboards and reports, as well as fully configurable analytics. Users may also utilize the web platform to receive useful insights and on-screen feedback via an interactive reporting feature.

To choose which reports are generated by Paychex—and view those reports—click on “Analytics & Reports” in the user menu. As with the main dashboard, you’ll be able to choose which tiles you want to view (and the order in which they’re arranged) by selecting “Manage Tiles.” To view all of the available reports, select “View All Reports” from the Quick Reports tile. Administrators can also create sets and favorites once they know which reports they access most frequently.

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A screenshot of the Paychex Flex dashboard’s reporting choices.

Administrators may modify reports by adding or removing columns, selecting between Excel and PDF, and including particular employee groups or departments, in addition to basic reports.

6. Hire new workers

You’ll need to add new workers to your Paychex database when they join your company. Navigate to the “Recruiting” tab in the left-hand menu if you’re using Paychex for both hiring and talent management. You’ll be able to utilize this Paychex tool to both recruit and onboard staff, with new employees being able to enter their personal information, direct deposit information, tax information, and other special information required by the employer at this time.

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Screenshot of the Paychex recruiting tool’s employee onboarding screen.

Alternatively, you may manually add an employee by going to the People tile on the user dashboard and choosing “Add Employee.” In any case, all of the employee data in your company’s Paychex database will be updated.

How to Use Paychex Flex to Manage Payroll

The procedure for actually conducting payroll through Paychex is really simple. The Paychex Flex software is used by both the Paychex Go and Paychex premium subscriptions.

To run payroll each pay period, follow these steps:

1. Go to the Flexible Payroll Grid.

When it’s time to process Paychex payroll, the Payroll Center makes it simple to see all of your employees, as well as the total number of checks, hours, and amounts due. To go to Paychex’s payroll section, go to the left-hand menu and choose “Payroll Center.” You’ll be sent to a page with a list of current payrolls organized by check date, company, status, and history.

Employee data will instantly appear in the Payroll Center if you utilize Paychex for time tracking and attendance. By pressing the down arrow next to the “Begin/Resume” option, payroll managers may easily import payroll data from other time management software.

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Screenshot of the Payroll Center’s home page

To examine a payroll, go to “Begin/Resume” and browse through the workers, search by name or ID, and see basic information like the number of checks and hours worked, as well as the amount to be paid. Individual payroll administrators may also create their own grid pattern based on their own requirements. Administrators may also use filters to see certain employee groupings, such as departments or hourly versus salaried staff.

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Paychex Payroll Center grid on a screen picture

If an administrator wants to check or change an employee’s profile, they may do so by clicking on the employee’s name in the grid. From basic personal information to direct deposit and tax information is available. Administrators may also use this section of the Payroll Center to see check stubs and contact workers with queries or payroll adjustments.

2. Examine and revise reports

Once you’re happy with all of the data in the payroll grid, click “Review & Submit” in the upper right corner. You’ll be routed to a page where you can view preprocessing reports and other relevant payroll details. This page also lets you choose from quick payment options, including real-time payments, same-day ACH, and standard ACH.

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Paychex Preprocessing Reports and Quick Totals review page (screenshot)

The Preprocessing Reports part of the website contains PDF and Excel versions of documents such as the Payroll Journal, Cash Requirements, and Job Costing reports. The Payroll Journal displays each employee’s overall gross and net pay, as well as department and business totals. The Cash Requirement document includes information on when money will be withdrawn as well as a detailed itemization of monies.

The Quick Totals area is just below that, and it allows administrators to see how many checks are being sent out for the pay period, the total number of hours being paid out (including overtime), and the overall payment amounts. Administrators may also see whether there are any people who haven’t been checked, in case they’ve overlooked someone.

If you need to make changes to anything in the reports, go back to the Flex payroll grid and select “Edit Payroll.” Before submitting payroll for processing, administrators may navigate back and forth between the reporting page and the payroll grid as many times as they need to.

3. Send Payroll to be Processed

Click “Submit Payroll” in the top right corner of the dashboard after examining the applicable payroll reports and ensuring that all of the information is accurate. Payroll will be handled within 15 minutes, however, administrators will have a limited time to make changes to the payroll information (this can be accessed from the user dashboard).

Once you submit, you’ll receive real-time notifications from Paychex indicating, in the first email, that the file has been processed and, in the second email, that the payroll reports are ready. You can then access reports by navigating to the “Analytics & Reports” tab in the left-hand user menu.

Paychex Payroll Administration Tips

Paychex makes utilizing payroll software simple by offering thorough setup help and customer service. Furthermore, the various automation and customizations make the payroll process simpler and more efficient. To get the most out of Paychex for payroll, follow these guidelines:

  • Leave the hard work to the implementation team: Paychex, unlike some other HR and payroll software, offers a full, guided setup procedure to its clients. This means you won’t have to manually enter all of your existing employee data or submit tax data for the current year. Instead, you’ll be assigned to a setup team that will take care of everything for you.
  • Utilize customizations: Paychex not only provides a powerful HR, payroll, and personnel management platform but also makes it simpler to use these features by giving a configurable interface. Make the most of this by customizing your dashboard to expedite your most frequent tasks, such as payroll review and approval or analytics and report review.
  • Customize Paychex reporting and analytics tools: Users may additionally customize Paychex reporting and analytics tools to make them more useful. Once you’ve determined what kind of data you require most often, customize your reporting dashboard by adding favorites. Choose which columns to include in reports and how they are presented using extra customization options.
  • Use the CARES Act tools: Paychex now has resources to assist companies in navigating the effects of the Coronavirus Aid, Relief, and Economic Security Act (CARES). Compliance assistance, HR coaching, cash flow management, and other tools are included. Paychex can also help businesses understand the Paycheck Protection Program’s forgiveness and tax ramifications.

Conclusion

You may use Paychex Go or a Paychex Flex premium subscription to make payroll with Paychex. Paychex Go and Paychex Flex both use the Paychex Flex software system, but Paychex Go can be set up in minutes. Premium Paychex Flex plans take additional lead time—up to a month—but you’ll get personalized assistance and customization throughout the process.

Frequently Asked Questions

What is Paychex Flex payroll?

Paychex Flex is a payroll service. It allows businesses to pay employees on their own terms.

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