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Paychex Flex: Extract and Required Data Guide

Paychex Flex: Extract and Required Data Guide

Guide users to access Paychex Flex, extract, format, and upload required payroll data.

This guide walks you through how to access Paychex Flex, extract the required data, and format files so you can complete your setup successfully.

Overview Checklist

Access

Data Extraction

Data Formatting

 

Requesting Access from Client (Check Team)

  1. Login to the Check Paychex Flex account using the credentials in 1Pass Vault
    1. 1Pass will also have security question answers
  1. Click on the dropdown at the top-left
  1. Click Add Company
  1. Input the Company ID
    1. This can be found in the setup request for that client
  1. Click Submit
    1. This will send the task to the client to approve Super Admin access

Granting Access Walkthrough

  1. Log into Paychex Flex account under the Super Admin credentials.
  1. On your Dashboard go to Task
  1. Click on People
  1. Search for Check’s user - Setup Admin
  1. Click on the name
  1. Select Access & Permissions
  1. Select Super Admin
  1. Make sure it says: Access to - Everyone
  1. SAVE
🚨

Only Super Admin can grant Super Admin access; follow specific steps to update permissions and ensure access is set to “Everyone” before saving.

Access Walkthrough if NOT going through Check’s Embedded Setup Team

🚨

If not going through Checks embedded setup process DO NOT use the setup@checkhq.com email. Use an email that you have access to.

  1. Log into Paychex Flex account under the Super Admin credentials.
  1. Click the User icon (top-right of the dashboard)
  1. Select Add
  1. Select User
  1. Enter the following information in the Basic Information section:
    1. First Name: Payroll
    2. Last Name: Setup
    3. Phone number: Have client use one that you will have access to for MFA codes
    4. Email: Have client use one that you have access to for invitation acceptance.
  1. Select the newly created user profile and change the Admin role to Super Admin
    1. Security Role: Super Admin
    2. Role Assigned: Company Admin
    3. Group Assigned: Everyone

Data Extraction Steps

Employee Demographics

Direct Deposit

Withholding

Deductions

Historical Payrolls

Company Tax Information

Tax Returns

Employee Demographics

To pull a report with employee demographic information (includes earnings rates and workplaces)

  1. Left Main Menu → Analytics & Reports → Live Reports → View All Reports → Employee Listings → Employee Demographic Data
  1. Update Filters, click the X next to “Status is not Terminated”
    1. This will now include terminated employees. Once report is ran you will be able to filter out termed employees from past years.
  1. Scroll down to the Details section → Click on Columns
  1. Click Add Columns
  1. Select the following columns:
    1. Company
      1. Company Name
    2. Contact Information
      1. Address 1
      2. Address 2
      3. City
      4. State/province
      5. Zip/postal code
      6. Personal email
      7. Work email
    3. Employment
      1. Business location
      2. Most recent hire date
      3. Organization (level 1)
      4. Status
      5. Termination Date
    4. Personal Information
      1. Birth Date
      2. First Name
      3. Last Name
      4. Middle initial
      5. Taxpayer ID (SSN or FedID)
    5. Compensation
      1. Pay Frequency
      2. Pay Rate (1-5)
      3. Ray Rate Custom Description (1-5)
      4. Pay Rate Description (1-5)
      5. Salary
  1. Click Apply
📝

After clicking Apply you can arrange the columns by dragging them to preferred order before hitting the X and downloading.

  1. Hit X to return to the main report page
  1. Select Download → Reports Details (XLSX)
🚨

If you download the CSV, the headers will disappear. Do NOT use CSV download

Direct Deposits

🚨

Paychex Flex does NOT have a report to see full direct deposit information.

Bank Accounts can be added in two ways when migrating:

  • Onboarding Links (most efficient and timely)
  • Manual Entry (manually enter each employee or use import templates)
    • You would need to go into each employee's profile individually to unmask and copy.

Check’s Embedded Setup team will only manually transfer direct deposit information if under 50 workers.

Onboarding links are recommended for ALL setups.

Withholdings

🚨

Paychex Flex does NOT have a report to see employees withholding elections.

Withholdings can be completed in two ways when migrating from Square.

  • Onboarding Links (most efficient and timely)
  • Manual Entry (manually enter each employee or use import templates)

Check’s Embedded Setup team does NOT manually transfer this information. Onboarding links are recommended for ALL setups.

Deductions

📝

There are NO reports that will pull per pay period deduction or benefit for workers. It is best to review a payroll journal and confirm on employee profile

If unable to find reports listed below the client may not have Benefits/Deductions/Garnishments/Child Support

  1. If you are ever unclear about what type of code something is, you can follow the steps below to confirm:
    1. Left Main Menu → Company Settings → Payroll → Pay Items → Deductions
  1. Other Report Option: (not all clients will have this report)
    1. Left Main Menu → Analytics & Reports → Quick Reports: View All Reports
    2. Under Health & Benefits Top Reports: Employee Enrollment & Deduction Summary
    3. The Employee Enrollment & Deduction Summary report will show who has deductions, Amounts shown on report are monthly NOT per pay period.
  1. Garnishments and Child Support (if applicable)
    1. Left Main Menu → Analytics & Reports → Quick Reports: Last Payroll
    2. Click on the most recent payroll run
    3. Click Garnishment Payment Service Confirmation Report
      1. This will show who but you will still need to go into their individual worker profile for Order details.

Historical Payrolls

Closed Quarter

  1. Left Main Menu → Analytics & Reports → Live Reports → View All Reports
  1. Search: Pay Item Details
  1. Open Pay Item Details
  1. Date Range → Click on the dropdown arrow
    1. Custom Date Range → select the correct dates per quarter (run for each closed quarter individually)
      1. Q1 (1/1 - 3/31)
      2. Q2 (4/1 - 6/30)
      3. Q3 (7/1 - 9/30)
  1. Under Details (scroll down) click on Columns
  1. Click Add Columns
    1. Select boxes for:
      1. Draw Amounts
      2. Fringe benefits amounts
  1. Download → Report Details (XLSX)
 

Optional Alternative Report (not all companies have this report)

  1. Left Main Menu → Analytics & Reports → Live Reports → View All Reports
  1. Search : Department Summary Data with Employee Detail
  1. Create Report
  1. Ensure you are on the correct company, if multiple companies in account
    1. Organization Units = All
    2. Input your date range
      1. For closed quarter, enter the following dates
        1. Q1 (1/1 - 3/31)
        2. Q2 (4/1 - 6/30)
        3. Q3 (7/1 - 9/30)
    3. Output Format is XLSX
    4. Layout = All Fields
    5. Run Report
 

Open Quarter

  1. Left Main Menu → Analytics & Reports
  1. Live Reports → View All Reports
  1. Search : Pay Item Details
  1. Click on Pay Item Details
  1. Date Range → Click on the dropdown arrow
  1. Click Preset ranges → Current Quarter
  1. Under Details (scroll down) click on Columns
  1. Click Add Columns
    1. Select boxes for:
      1. Check Date
      2. Draw Amounts
      3. Fringe benefits amounts
  1. Download as Excel (if the file saves as .XLS export to .XLSX)

Optional Alternative Report (not all companies have this report)

  1. Left Main Menu → Analytics & Reports → Live Reports → View All Reports
  1. Search : Department Summary Data with Employee Detail
  1. Create Report
  1. Ensure you are on the correct company, if multiple companies in account
    1. Organization Units = All
    2. Input your date range
      1. Use the check date for Start and End dates
    3. Output Format is XLSX
    4. Layout = All Fields
    5. Run Report

Company Tax Information

  1. Left Main Menu → Company Details → Taxes Tab
  1. Here you will be able to see Tax ID, Rates, Filing Frequency for Federal, State, and Local Taxes
    1. Tax Topics → State and Local → Federal Taxes
    2. Tax Topics → State and Local → State and Local Taxes
🚨

Washington Clients:

Washington Labor & Industries (L&I) is Washington State's workers' compensation insurance program, and unlike most payroll taxes that are wage-based, L&I premiums are calculated on hours worked — meaning the state requires accurate hour tracking to properly assess employer and employee premium liability.

  • L&I Risk code can be found in the workers profile under Workers Compensation.
  • SOC codes are listed on the SUI wage detail quarterly return

Tax Returns

  1. Left Main Menu → Analytics & Reports → Quick Reports → View All Reports
  1. Under Tax Top Reports
    1. 941 - select the quarter(s) you need, Download
    2. Quarterly Report - select the quarter(s) you need, Download
    3. SUI Return - select the quarter(s) you need, Download
        • If starting in Q1, pull the prior quarter's return (Q3 or Q4) to confirm tax information.
        • If starting mid-year, pull every closed quarters return in the current year.
🚨

Obtaining closed quarter(s) tax filings is required and will allow you to tie out each quarter in current year to ensure balancing with the transfer of historical data.

Tax documents serve dual purpose for setup:

  • Allows you to tie out closed quarters in the current year when importing the historical data.
  • Provides required information to complete the Tax Parameters.

Data Formatting

Refer to Help Article - Data Formatting for details on how to format reports for a smooth import experience.

 
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