Thanks for getting back to this thread, @userhuini.
What my colleague above referring to is that if your invoice payment is deposited in the Undeposited Funds account, you can use the Bank Deposit feature to transfer the payment to your real-life bank.
The Undeposited Funds account keeps a record of payments in QuickBooks until you physically deposit the same payments at your real-life bank.
That said, you can create another line to record the bank charges with a negative amount once you deposit the invoice payment. This way, it will reduce your deposit amount. Just follow the steps provided by my colleague above.
In addition, you can check the following articles below for additional reference:
Once your bank transactions are on the Banking page, you can now match and categorize them the ones you've entered in QuickBooks.
Let me know how else I can help you with QuickBooks by adding a comment below. I'm more than happy to lend a helping hand. Keep safe!