This is a valuable reprint of Janet Taylor's article in the TTA Update that I think you'll find useful in handling PTO:

Did you know if you are using both Jonas Timekeeper and Jonas Payroll you can post Holiday/Vacation/Sick pay in Timekeeper and pull it over to payroll? This means each supervisor can enter these hours for their staff when the time is requested by the employee.To enter the time, go to Timekeeper / Processing / Maintain Time Data. Put in the proper department and hit enter for the Week Ending. Click Add a New Record. Seq # should be 2 so it will not conflict with the current day's record if the employee is clocked in. At the bottom, use the drop-down to select the Other Hours Code H04, H05, H06 that corresponds to your Holiday Pay, Vacation Pay, or Sick Pay code. The Other Hours Rate Factor would be 1.0 for straight time, 1.5 for overtime and 2.0 for double time.

Clicking the T/A button will display the employees’ accrued annual leave if you use the JONAS Time & Attendance program.