PAYG is coming from the Prefill from the ATO. 

To stop the system from prefilling PAYG, please uncheck the box for "Manage Activity Statements" via Client Settings>Tax Returns

If still does'nt work, you can manually add a negative amount.

Example, The Q4 amount is supposed to be a minus as it was refunded:

Add the -$666 to arrived the correct  total amount.