One of the product limitation of GST center is that we cannot record a payment of more than what is showing as due in the GST center. As a work around, please follow below steps
Step 1: Create a clearing account and name it as "petty cash" with account type set as Cash and cash equivalents - Related steps on how to create a Petty Cash Account
Step 2: Pay amount that is due in GST center from this newly created clearing account "petty cash" account.
Step 3: Transfer full amount (that was paid to ATO including over payment) from Bank account to petty cash account.
Step 4: Now user has 2 options
a) Leave the over payment in petty cash account and use it for next BAS. OR
b) Create a journal entry to move over payment from petty cash to ATO clearing account to mimic ATO account. This will then show a credit and can be used for next BAS
Note: You will need to do a reversal journal before applying payment for next BAS if option b is used.