@bottomlineusa 

"First, not all customers pay their invoices in full, for various reasons. Also, it is important to apply payments to invoices in the amounts the customer intended, to match their records."

Of course.  I was a corporate controller for 20 years (now working on my CPA) and payment terms (and how those payments are applied) should always be dictated by the company providing the product/service, not the customer.  That's part of the agreement a customer makes when applying for credit terms.  But, I get your point of wanting to see the amount of a single payment applied to multiple invoices.