When we create an order, it's for custom clothing which will be manufactured.  We take a 50% deposit up front.  We have limited choices because we are unable to tie a deposit (i.e. credit memo) to a specific sales order.  

The correct action is to receive a payment from a customer so it hits the Undeposited Funds account and is reflected as a negative on the Accounts Receivable, and therefore recorded as a deposit to the customer.

The problem is that we can only record that to the customer's account as a credit memo, not to the sales order, and there's no way to connect the two together.

If we use the hack, which is creating a "deposit item" then we have no accounting record of that money, only a "note" on an open sales order.  Until we invoice the order, which won't happen often for a few months, that money sits in limbo, and we are liable for it if there's a problem.