After-the-fact payroll requires an Enhanced Payroll for Accountants subscription.
If you select this preference, when you enter the employee name in an after-the-fact paycheck, QuickBooks copies the amounts for wages and withholdings from the last paycheck entered for this employee. QuickBooks then calculates amounts for taxes other than withholdings, and gets deductions, additions, and company contributions from the payroll items created in the employee record.
If you don't select this preference, QuickBooks gets all amounts (including wages, Fed W/H, and State W/H) from the payroll items created for the employee in the company file.
Where can I find this preference?
After-the-fact payroll overview
Enter and delete after-the-fact paychecks