There may be circumstances in which you are going to require a prepayment (i.e. deposit) from your customer. There are a variety of reasons for this practice (new Clients, custom work, a Client with a bad track record in paying on time, etc.) If you need to account for a Customer Deposit here's how. In this context, we are applying a general deposit on account to be applied against some future invoice. This deposit is not tied to any specific invoice yet. If you want to Invoice a customer now and collect a pre-payment before shipping, you may want to look at the Deferred Revenue feature.

If you have already entered a Customer Deposit and you need to know how to apply the Deposit to an Order then check out this article on How to Apply a Customer Deposit.