QuickBooks Point of Sale & QuickBooks Enterprise

We spoke briefly yesterday on your website, but I was unable to get an email out to you yesterday.  I've been using QuickBooks for a few years now, so I like to say I'm fairly knowledgeable, but I've ran into a problem that I haven't ever encountered, until recently.  We are using QuickBooks Premier Manufacturing and Wholesale Edition 2009.  We have a customer (customer A) that we sell to wholesale.  They then sell the product to their customers.  They send us the orders and we drop ship for them to their customers (customer Z).  Once the product is shipped, we invoice customer A.  Customer Z pays customer A upfront and then customer A pays us pretty quickly.  Customer A is set up as a customer while customer Z is set up as a job.  Just recently we had a few returns weeks after we received payment for it.  When we get a return, we create a credit memo and then send it to customer A.  Customer A then refunds customer Z.  Since we have already been paid for said invoice, we technically owe customer A which is why we create the credit memo.  But because we are constantly doing business with customer A, we sent them the credit memo and then they subtract the credit memo from a check they send us.  There are several credit memos but just as many invoices on this particular check.  The problem I run into is that I cannot apply these credit memos on the "receive payments" screen because they have already been paid for and therefore are not even listed on under customer A.  I have a check for $2,000, but I need to apply payment to take care of $4,000 worth of invoices.  The remaining $2,000 needs to be applied to the credit memos, but like I said, they do not show up when I receive a payment.  I'm lost at this point.  If you could send me in the right direction, I would greatly appreciate it.