Hi Theo,
One way you can do this is with a custom extension where your Microsoft Partner can develop it for you.
Please let me know if you need any assistance with this.
It shouldn't be too much, as a specification you can ask them to do the following:
- add 2 new fields in the payment methods table/page with:
* the %value you'd like added to the invoice
* a GL Account to track these charges
- on before post sales document event of document type invoice, create a new line with the %value * total amount of the invoice. This can go to the GL Account selected on the Payment Method associated with the invoice.
Cheers,
Robert
Please verify my answer, if you find it useful, that way others can find this solution easier!