What do you do if a Sales Order is Billed but you need to attach a customer deposit to it? The Sales Order does not show up in the Customer Deposit's Sales Order dropdown

@Jared Fraley On the customer deposit, click on Apply and apply that deposit to the Invoice generate from the SO.

That solves the accounting problem, but unfortunately not the balance due on the sales order problem (which is not that big of an issue), thank you!