I can help you get around with your concern, Dane MTS.

You can receive the invoice payments normally, deposit it to Undeposited Funds, and deduct the fee from there. Then, you can match the deposit to the downloaded payment.

First, here's how you can receive the invoice payment:

1. Click the Plus sign (+) icon, then choose Receive Payment.
2. Choose the customer, then the invoice.
3. Enter the amount received.
4. Click the Deposit to drop-down arrow, then choose Undeposited Funds.
5. Click Save and close.

Then, deposit the payment and add a line item for the fee. Here's how:

1. Click the Plus sign (+) icon, then choose Bank Deposit.
2. Select the payments.
3. Under Add funds to this deposit, add the customer, then choose an expense account for the fee.
4. Enter the fee as a negative amount.
5. Click the Account drop-down arrow, then choose the bank account.
6. Click Save and new. 

Lastly, match the deposit to the payment.

If there's anything else that you need, please feel free to drop a comment below.