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In QuickBooks Online (QBO), we can add the fees on the bill so it'll automatically match the payment amount or check. If you haven't added the fees to the bill and your bank account is connected to QuickBooks, just resolve the difference when matching the transactions. Here's how:

1. On the Banking page, go to the For Review column.
2. Look for the downloaded transaction (check/payment).
3. Click on it, then tap on Find match.
4. Select the bill under the Select transaction to match page.
5. Hit the button in between Resolve and Difference at the bottom of the page.
6. Enter the fees under the Add resolving transactions section.
7. Press Save.

For more details about this one, see the Categorise and match online bank transactions in QuickBooks Online article. Once done, you can start reconciling your account in QBO.

Feel free to visit our Banking page for more insights about managing your bak feeds transactions.

I'd like to know how you get on after trying the steps, as I want to ensure this is resolved for you. Just reply to this post and I'll get back to you. Take care always.