Most of my customers pay with credit cards (not present) that are manually entered in "receive payent". Once the payment is made/processed the actual amount that ends up in my bank ends up less due to credit card fees (I understand it's illegal to charge a fee in my state to off-site this fee). How do I record/receive payment on the lesser amount - the invoice shows an outstanding balance and the transaction will not "match" once the payment is processed and is in my account??
I can help you with proper fee recording. First thing you probably should do is post the payments to Undeposited Funds instead of directly to banking. Chances are the card processor batch deposits a days worth of multiple payments, and deduct the fees from the deposit.
Next, for each real deposit you will create a deposit, selecting the gross payments that are unused in it. Now, before saving it, add a line item for Card processing fee expense as a negative. This will reduce the deposit to equal the net as well as post your expense properly.