There should be a much simpler way to take down payments on projects than a retainer invoice. This just complicates and confuses clients. A simple field directly on an invoice for a percent or $ amount down is all that is needed. This is already there but is shown as an adjustment or discount. Just change this field to Down Payment and account for it as such.

This way the client can easily see the total and the required "retainer" instead of sending them 2 forms and confusing the matter.