Hello hbscoresby@optus,
You can add the bank transaction as an expense under the taxes paid category to be able to reconcile your bank account in QuickBooks Online. Under For review of Banking page, you can select Expense as the transaction type, and under the category select the taxes paid or choose an account on how you wanted to track the BAS payment.
For the usual process on how to prepare and lodge the BAS in QuickBooks Online, after you've prepared and lodged a BAS period you record a BAS payment, and then match the BAS payment to the bank transaction. You can also check this article to learn more: How to lodge a BAS or IAS in QuickBooks Online.
Furthermore, we'd also recommend contacting your accountant to get more information on how to account the bank transaction to the ATO to not mess up your books.
You can always post your questions here anytime. We'll be sure to get back and help you.
