I use QB with the Chase merchant account and the online billing. I have credit card, PayPal, and check deposits that are all getting deposited to the same account.
I just go ahead and let QB enter the full deposit not worrying about the discount fees but being careful to not lump deposits of different kinds of payments together. When making the deposits in QB, it helps out later if you change the memo field to "Credit Card", "PayPal", "Check" etc. according to where the deposit came from. When I have my bank and Chase statements, I reconcile my bank account.
During the reconcile, I take the bank statement and look at the date of the last Chase deposit. I mark every "Credit Card" deposit before that date as cleared. I then do the same with PayPal deposits.
I then continue as normal clearing the debits and credits that were from checks that show on the bank statement.
Provided there are no errors, when done, my reconciliation is off by an amount that is the amount of the discount fees, PayPal fees, and merchant monthly fee. I let QB make an "adjustment" and it enters that in the register. I then open the register and change the account that the adjustment was enterd to as an expense: "Merchant Fees" (or whatever account you set up for that).
This is not too scientific but I've not yet had a problem with doing it that way. After a few months, I got a feel for about what the total amount of the fees should be. If the adjustment is out of the normal range, then I go look for an error somewhere.
You do have to make sure that you allow for your QB register and your actual bank balance being off by that adjustment amount at the end of the month. If your normal total merchant fees are around $40, just be sure to keep at least more than that showing in your QB register and you will be fine.
Hope that helps.