If a Refund from your BAS has come from ATO (or is due and you want to enter it now), here are the steps:
Go to Banking Command Centre
> Pay from Account (where paying from)
>ID# leave auto # >Date
>Memo: ATO BAS Y10 Q2 Refund
> Acct# in lower section to allocate: GST Collected and type in the 1A NEGATIVE amount from the BAS form, next line GST Paid and type in1B as POSITIVE, then PAYG Liability (or Payroll Liability) as NEGATIVE. Use NO TAX CODES. The Total Allocated (in the lower part of the transaction) should match the Amount in the top yellow, top RHS >Record.
Click on the image below to see the detail.