Payroll - pay frequency

Hi Anewbee 

The Pay frequency of a pay determines what employees will appear in the list of employees to pay, the (default) period dates and the tax table will be used.

If it was me I would be processing a separate pay run for that employee i.e. go to Payroll>>Process Payroll>>Ensure that on Step 2: Employee Pays that employee is not ticked in that window. You would then go back through the Process Payroll process again and on Step 1: Pay Period ensure that you select Process individual employee before selecting that individual employee. You can also add in the respective pay period dates as required. It would then be a matter of ensuring that you have the appropriate pay amounts for that short period of employment including the PAYG component (best to speak to the ATO about what tax table to process that under).