When I receive payments, I would like to include the credit card processing fee when entering the customer Invoice payment.

Invoice payment allows for "bank charges" to be specified, but they are hard wired to use a generic bank charges account, which is not applicable if the charge is part of Cost of Goods Sold (COGS) - I would like to have the flexibility to change this, so that it goes to a (COGS) credit card charges account.

A benefit of this, would be that I would not have to enter a separate transaction to mop up the difference between the customer charge and the amount received from square (which is the processing fee), which remains in the Square clearing account.

In the above context, the integration with Square has automatic invoice generation turned OFF, and customer payments are being reconciled individually.