Business case - the user needed a way to invoice customer for fees the user incurred as a result of receiving a credit card payment from the customer, without including the fee as a line item on the invoice.
Solution - use the Miscellaneous field on the transaction (this works regardless of whether you're using Sales Order Transaction Entry, Invoice Entry, or Transaction Entry) to invoice the fee to the customer.
Sales>Sales Transaction Entry
* click on image to enlarge
In Posting Account Setup, Series = Sales, set the account on the Miscellaneous line to be a revenue account, or whatever account you find appropriate, so the distribution occurs automatically.