"How does this work when you try to match it with the bank transaction? I matched a wire payment with an invoice and it doesn't seem to let me change the amount received because it's linked to my bank fee"

Make the entry for the Payment yourself, first. Process the receive payment for the full amount the customer paid. Not for the Net to Banking, because the customer didn't incur the fee. You incurred the fee.

The customer owes $200.

You process a Payment for $200.

You put this to Deposit, and on the next line, using negative, post the bank fee expense. Now you have a Total Net reduced deposit.

Now electronic banking can match that same total.