Bank Charges currently exists as a sales code, I believe it is 7901 but does not then raise the relevant charge as a separate purchase.
We are unlikely to build an automated function to do this into KashFlow, I would suggested discussing with your accountant the best way to manage this?
I added a bit more general suggestion in http://kashflow.uservoice.com/forums/288652-requested-features/suggestions/8268183-multiple-credit-debit-accounting-codes-in-one-tr