Hi @Dsalkeld
Would this be the 1% you’ve set to charge the customer (e.g. 1% above the price of the invoice)?
If so, as the customer has paid it, it’s automatically assigned to the client’s account. How you handle it from there is up to you, but a common scenario would be to modify the invoice(s) they have paid and add a line in for it (and then paying the balance from credit), or bulking them together in an invoice at month’s end (for example).
Take a look at this article for more information:
http://community.quickfile.co.uk/t/adding-an-automatic-charge-for-card-payments/8880#3