Retainer Invoice payment not showing in Invoice

Retainer Invoice payment not showing in Invoice

Hi - When I get a new client I have them pay me half down.  I send them a retainer invoice (and apply to their invoice) and when I'm done with the project I send the main invoice.  But I can't figure out how to show the retainer paid amount on the main invoice.  For example I charge someone $650, they pay the retainer of $325.  I bill them when I'm done for the remainder, but the invoice shows the balance due to be $650, not $325, even though I have applied the retainer to this invoice.  Am I missing something?  Do I have to create a project?  Thx.