Trouble with this is that in Quickbooks we can see the payments applied at the bottom of the invoice so if we make a line item then the balance due will be off.  I tried it.  I guess you could 1st make the line item send the invoice go back delete the line item and then take the payment out but that is very cumbersome.  I just had this happen.  I had a client who had an outstanding credit and I took it off her next invoice but it does not show on her invoice only on mine.  It seems like if we can see the true balance due then the clients should be able to as well.