"A customer over paid on an invoice and it was marked to leave for use at a later time. Then a credit memo was created for the over payment"

That is the error. The overpayment already created negative AR. They just Doubled the negative.

"This was from a previous year so I am not sure how to go about taking care of this without it changing the financials for 2015. Can someone tell me how to clean this up?"

You need an Invoice for this. Whatever was used on the credit memo, use that same Item for the Invoice and then apply the credit to this invoice. Date it current.