Detailed Payment Report

Our A/R department is looking for more information on the payment reports that print from Netsuite.  Consider the following case:

A customer has a number of outstanding invoices.
The customer sends in a check, but asks that we not yet apply it.
The check is entered as a deposit into Netsuite.
A few days later, the customer sends another check, and tells us to use all the checks they've sent to pay invoices.
Our A/R department uses the check and the deposit together on a single payment, then prints the payment report.

The problem is that the payment report will show only the invoices that were paid by the second check.  The payment report does not reflect the invoices that were paid using the deposit because we did not actually receive any "new" money by it.  This causes a lot of confusion for A/R, since they apply X dollars to invoices, then get a printed payment report saying Y dollars.