When you pay GST in QuickBooks , you are recording the payment against a specific GST period; you are not actually transferring money to the ATO.
You can also record installment or partial payments this way.
QuickBooks will show you how much you owe and allow you to view your GST payment history. For payments, you must also make a payment directly to the ATO.
There are two ways to record a GST payment that will be applied as an installment payment towards an upcoming lodgement period. From the GST page:
If you accidentally use one of these options to record a payment against an upcoming lodgement period when you meant to record it against an existing lodgement, the amount will display on your next lodgement instead.
To correct this inaccurate filing:
Once the adjustment is complete, you will have a GST adjustment in both the bank account and in the GST Payable account.