This method causes problems.

The first problem is that it reduces the value of the total sales order in the list of sales orders.  A $1000 sale with a $500 negative "deposit item" reduces the value of the order by $500 and then the list of orders shows a $500 order with a $500 balance when it's actually a $1000 order with a $500 deposit.

The second problem is that the deposit doesn't actually hit its associated account until the sales order is invoiced.  This is unacceptable when recording customer deposits.  There is no way at this point to validate or verify that a custom has a deposit on their account, and there's no accounting of that deposit.

Is there a way to attach a payment to a customer account and then use that deposit on the account towards an invoice while also keeping a reference to the order which the deposit is intended to be applied?