I needed to do this as well, and figured out a way (no thanks to QuickBooks). You do not need to turn off Auto Payroll to update your employee's time off.
1) Go to Payroll
2) Click on Overview
3) Click on Auto Payroll details
4) Click on Update upcoming payroll
5) Enter the number of Sick Pay Hrs (or PTO or Vacation Hrs). In the Memo section, record the dates time off was taken.
6) Click Save for Later.
You can also click on Preview Auto Payroll so you can ensure the time off was recorded accurately.
Your payroll should run automatically as long as you made your updates before the auto payroll cutoff date.
