To begin paying out an employee's leave check which payroll calendar you are processing. You can do this by taking the follwoing step.
Payrun --> Employees --> Employment

This is important so you can schedule leave accordingly. In this case, we are processing a Fortnightly payrun ending on December 2nd.

Once you have clarity on the period you are scheduling, move to the leave tab.

The first thing you will want to check is an Employee's Leave balance.

Once, you have written down the leave balance (or if you are an elephant, remembered it) click on Add Leave Application.

You will then be prompted with a pop up where you can enter when the employee's leave dates.

Select the dates so that the pay period is the paycycle you will be scheduling later on, and modify the total amount of hours so that the amount of hours the employee will take match those that he has in the balance (remember to include the hours he would accrue during that final period!).

Once, your leave application has been updated you head on over to pay runs and process the pay run

On the pay slip you will notice that the leave you have just scheduled is now included in the earnings line.
Next, adjust the ordinary hours worked to reflect the correct hours work.
In my example I have changed the hours to 0 as I am only paying out leave balances in this pay run.

Note:The employee will be accruing additional leave for this last period, so remember to include it in the leave scheduling.

NOTE: IF YOU DO NOT WANT THE EMPLOYEE TO ACCRUE LEAVE DURING THE FINAL PAYRUN, THEN YOU SHOULD DELETE THE LEAVE ACCRUAL LINE.

Finally, there is a manual adjustment you need to do for Super, since unused Annual leave is subject to tax, but not subject to super.

Since Paycycle requires you to have an SGC line, you need to enter 0% in the "Percentage" box where traditionally there is 9%.

Next hit SAVE and Post the Payrun.

To make sure everything has gone smoothly head back to the employee's Leave tab and ensure that the their leave balance is zero.