Customers can't pay their invoice in store at the POS Register

We create invoices for customers and many pay online but quite a few prefer to come into our brick and mortar store and pay in person. There is no way to access their invoice from the POS register. Our work around has been to create a ‘product’ called payment for custom order and put it under their name. Then we have to go to the office at the back of the store and find their invoice and mark it paid. But the system then thinks we received that amount of money twice and the daily totals are off. This isn’t really working.