Note that the accounting on Customer Deposits takes a little bit of getting used to. The GL impact of a CD is a debit to Cash (or undeposited funds) and a credit to a system-generated account, Customer Deposits. This impact is not customizeable as far as I know. When you apply it to an invoice a kind of "background" transaction is generated automatically called a Deposit Application. The GL impact of this is a debit to Customer Deposits (clears this balance for the amount of the CD) and a credit to AR (clears this balance for the amount of the invoice).