The problem is not solved.

There seems to be no provision to attach a set $$$ amount in the form of a customer payment to a specific sales order such that when the sales order is converted to an invoice, it simply uses those funds.

The only way we can get the books to be accurate real-time without a myriad of manual entries is to receive payment and generate a credit memo for use later, which means we have to somehow reference exactly WHAT Sales Order that payment is supposed to be paying for.  This can get messy if the same customer orders two of the same thing on separate sales orders.

What we really need is the ability to create a sales order, send a link to a payment interface to the customer for 50% of the order, let the customer securely enter their CC info, charge the card and automatically attach those monies directly to that order so they can be settled in the future when the order goes to invoice.

Right now, there's just too much margin for error in the process because there's too much manual maintenance required.