To record a payment made to the ATO for your GST on the same day, while you are not using the GST centre in QuickBooks Online, please follow the steps below:
1. Click on + New button
2. Select Journal Entry
3. For GST payment to ATO, select GST Liabilities Payable account and enter amount of payment in Debit column.
4. Select the bank account the payment has came out from in the second line of the journal and enter the same, payment amount in the Credit column
5. Click Save and Close
6. If bank feed is connected, this journal can be matched with payment record came through via your bank feed.