Hi @Milo123 ,
QB always creates a bill for the amount owing when the return is filed. It will only show now as a bill in the Accounts Payable if you did not use Accounts Payable to pay the original amount owing. How did you pay the bill? Did you use the 'Pay Bills' feature or did you just write a cheque from your Bank account and post directly to the GST Payable account? If you've written a cheque from the bank account directly, you can go back to that transaction, open it, change the account to your 'Accounts Payable' account, tab across to the name, and choose your GST tax vendor (Receiver General, or CRA, or whatever you have called it). This has now created a credit in your AP for that vendor. Then go to Pay Bills and apply the credit to the outstanding bill amount. If I've misunderstood your situation, please let me know.