Thanks for posting in the Community! Once you lodge your BAS electronically through QuickBooks Online, it'll be processed automatically. On the other hand, BAS/GST payment needs to be done manually as electronic payment is not available.
Here's how to record a GST/BAS payment in QuickBooks Online:
Go to GST, then navigate to the To Do tab.
Select Record Payment on the activity statement you want to record a payment against.
Enter the amount paid.
Select the Account the payment was withdrawn from and the Date of the payment.