Hi;

I beleive you started wrong way initially. When u have an invoice=50$ and a customer pays 100$, this invoice is and should be fully recondiled as its full amount is paid, another 50$ is an advance payment for future invoices, which means that in Customer Payment Document, when u register this 100$ payment, 50$ invoice will be reconciled and u get difference amount=50$. You should choose the option: "Reconcile the payment balance" and choose the account from accounts list: "Advanced Payments Liability"(Or else u call it). What happens is that u will have the liability of 50$ created to the customer in terms of received advance payment. So the journal Entries will be:

Debit: Bank - 100$. Credit: 1. Account Receivable  - 50$ 2. Advance Payment Liability - 50$.

Next time u sell smth to this customer, suppose 60$ so that he has to pay only 10$ more, when u open customer payment document, u will see this 50$ payable in it. U click on reconcile bulean of this 50$ and register the 10$ payment, what happens is: 50$ avance is reconciled and 10$ payment is registered. Journal entries will be as wollows:

Debit: 1. Bank-10$ 2. Advance Payment Liability - 50$. Credit: Account Receivable - 60$.

I think this info might help you.