Actually that is not how quickbooks processes transaction payments. QB merchant services do not take fees out of the deposits, they deduct fees from your bank account a few days after the deposit is processed so the deposit is the exact amount that is receipted in quickbooks. In addition it also carries the customer name invoice number and id from QB merchant services and displays it but wont auto match.  When you look on QB it even says the name of the client, the invoice number it was paid for. QB batches the payments on a daily basis not sure if this throws it off but you would think QB should be able to automate from their own payment system to recognize invoice and client as the information is right there displayed it just does not automatically do it. Same with checks, mobile deposits etc. If I simply treat it as a deposit then QB says to me that is extra income so I have to some how match multiple deposits to payments even though its done in QB already. Makes for much longer and harder process than using a pen and paper supposed to simplify life not make it more difficult.