Hi @Betty
I'm not sure if this would help, but I think if you take a look at this, this would help separate the credit card charges and what you charge the client:
I think if you're looking at working out the net amount per invoice, perhaps tagging card fees to an individual invoice, and then tagging invoices to a project could help, although bear in mind that this would increase the number of ledger entries you create.
Take a look at this topic for help with project tagging:
Does that help? 