Quickbooks Desktop is easy. (im still trying to figure it out for QBO)
When in Desktop, go to banking receive payment. Select your customer, date, amount of deposit and reference. Select the invoice(s) being paid. Make sure your invoice is "highlighted" and select Discount/Credit on the top. Make sure yo are on the discount tab. Enter in the amount of the fees and select the expense account (example credit card fees) that you want to the expense recorded in. If you have mulitple invoices, you can apply a portion of "discount" to the invoices by repeating the steps, or you can apply the entire discount to 1 invoice. Now all your invoices should be paid in full in A/R. And when you go to do your bank reconciliation, the actual amount deposited in the bank will show up in the deposits section. (not a credit and a debit that you have to manually net to get the total deposit)
