You are not able to do this if you are collecting payments in quickbooks via QB Merchant Services.
We used Freedom Merchant as our external processor. Freedom Merchants will give you a payment link that goes in the body of the email when you send an invoice out from QB. The customer clicks on the link to make the payment and the fee is added when they click on the link. When the client pays you get a notification AND it marks the invoice paid in QB through their integration. You can contact [email address removed] as he was quite a bit of help with the setup.
I struggled with QB and the processing fees solution for a long time. Freedom Merchants really helped recoup those costs. However...I have since moved to a custom order management software that automatically adds the fee on the purchase and then we now push the final order to QB just for bookkeeping purposes.
QB Merchant charges excessive fees and on top of it they charge the full credit card fee on refunds too. It really was so much good money wasted.
I wish you luck as we small business owners do not have much time to jack around with this stuff but it is important to find time to help your bottom line.