Hi grantlisa-brydon,

Thanks for posting in the Community!

When you finalise a pay run, a payroll journal will be exported to QuickBooks Online. PAYG Withholding amount will be automatically allocated with a code BAS-W2 and will be included on your BAS lodgement. 

When you mark the BAS as paid in the GST tab, the system is designed to move the PAYG Payable amount into the ATO Clearing Account to then be offset by the match in the bank feed. 

For your reference, you can check on this article: GST Chart of Accounts and Lodgement Journal Overview.

Feel free to drop a comment below if you have any other questions. Have a great day!