To simultaneously process payroll for groups of employees who are assigned to different pay cycles, enable the Payroll Data Entry batch feature on the Entry tab in Payroll Options. Then create a separate batch for each pay cycle. For each batch, use the Auto Pay feature as you normally would.

For more information about the batch feature, see Payroll Batches.

To learn more about processing payroll using the Auto Pay feature, see Set Up and Pay Employees Using Automatic Earnings Codes.