Hi there, Monica.
You can record a period HST payable as filed and paid in QuickBooks even if you process it through your bank account.
Here's how:
- On the left menu, head to Sales tax.
- Scroll down to the Filings section.
- Look for the HST payable period you already filed and paid.
- Click Prepare return.

- Review everything then click Mark as filed.

You'll now see the HST status is prepared, filed, and paid, which means it's now recorded in your QuickBooks account.

Furthermore, you can consider switching to automated sales tax in QuickBooks Online. With automated sales tax, QuickBooks automatically calculates sales tax based on what you sell, where you sell, and where you ship.
You can always leave a reply if you need help with anything about sales tax or any other concerns in QBO. We're always available to assist you.