I do it differently, there are two ways
1. create a service item for the fees linked to the expense account, use that item on the invoice, qty is negative one and enter the amount of the fee, save and receive payments, deposit, then download and match
or
2. receive the full amount, then use make deposits and at the bottom of the form select the expensed account and enter the fee amount as a negative number, then deposit. download banking and match