We probably need some clarification here. First of all, are talking about AP or AR? It sounds like AR but I cannot be certain. If it is AR then we have some terminology issues here. You cannot apply a payment to a credit memo. Payments are only applied to invoices or debit memos. If I assume you mean to apply credit memos generate to the customer and then apply the payment to what is left you might be able to use the AR auto payment menu item to do that but that process has a couple of things to be aware of.
First of all, it cannot directly be done on one customer. It can only be done at a statement cycle level so, if you use it specifying the statement cycle id that this customer belongs to, it will run the process against all customers that are a member of that statement cycle and might result in an application of a credit memo or outstanding payment to an invoice you did not want paid at this time. You can get around that by creating another statement cycle (kind of a temporary one) and move this customer to that temporary statement cycle and then run the auto payment application process against just that statement cycle id. When you are done, move the customer back to their normal statement cycle id.
The next possible roadblock is that this process will pick up unapplied payments and open credit memos for the customer in the reference number order and apply each credit to the oldest invoice or debit memo working toward the most recent invoices and credit memos. Using this process you cannot direct specific credits to specific invoices. You can only do that using the payment application screen and selecting one credit memo at a time and applying it to particular invoices. However, if you just want to apply all open credit memos and all unapplied payments and you do not care what goes to what, this process will do it quick and easy for you.
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