When applying retainer invoice payments to an invoice, is it possible to apply those payments to a specific income line item?

Here is a typical situation for us. We are a service provider, and our invoice income is divided between Labor and Reimbursable Materials. We purchase supplies specific to a project (Reimbursable Materials income) and ask the customer to reimburse us for those materials up front by creating a Retainer Invoice, while billing for the labor and any additional materials at the end of the project. Once a final invoice is created, when the Retainer Invoice payments are applied they seem to be arbitrarily distributed between the two income line items. When viewing the final invoice the payments are applied correctly to each income line item, but when viewing the payment itself under Sales > Payments Received or in any reports such as Profit and Loss, General Ledger, etc. the payment amount is incorrectly split between the two income line items.

Ideally I would like to be able to choose how much of each Retainer Payment goes toward each Income Line Item when it is applied to the final invoice.

Am I missing something, or is there a better way to apply pre-payments/down payments in this kind of situation?