Are you trying to process or apply leave to your employee's pay run? If so, you can apply the leave taken using the Take Leave option. Let me show you how:
Click on Employees tab.
Click on New pay run.
Select the Pay schedule, pay date, pay period ending date.
Select the employee to see their details.
Click on Actions, and click on Take Leave.
Select the Leave Category, and enter the Hours Taken.
If you have not set up the specific leave category, you can go back to Payroll Settings, and click on Leave Categories to add a new one.