Bonus: Paying separately from regular paychecks (bonus run)

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You have a couple of options when paying employee bonuses:

Pay a bonus separately from regular paychecks

Go here.
(Or click the Payday tab.)
If necessary, select the pay schedule.
Click the Regular Checks drop-down arrow, select Bonus Checks, and then click Go.
Click the checkbox next to any special settings you want to apply to this bonus; for example, calculating net-to-gross or supplemental taxes. If you want different treatment for some employees, do more than one bonus run.
Set the pay date, if necessary.
Select the checkbox next to all of the employees you want to include in this bonus run.
Enter an amount for each employee you want to pay, and then click Create Paychecks.
Review the bonus check, and then click Approve.
Print checks or stubs.