Hi David,

Thanks for posting in the Community! 

If you create an invoice or sales receipt in QuickBooks Online we can match it to the transaction downloaded from your bank so we can allocate the difference to bank fees. Here's how to resolve a difference when matching an invoice to the payment downloaded from your bank. 

1. Go to Transactions, then select Bank transactions.
2. Select the bank account with the transaction.
3. Locate and select the relevant transaction on the For review tab.
4. Select Find match.
5. In the Match transactions window, tick the box for the appropriate Invoice.
6. Select Resolve to open Add resolving transactions.
7. From the Category dropdown, select the Bank fees expense account you created.
8. Enter the Amount of the bank fee.
9. Select the applicable GST.
10. Select Save.

For your reference, you may also check this article: Account for bank fees when matching transactions in the bank feed in QuickBooks Online. 

Let me know if you have any other questions with. I'll be around to help you.