I was hoping to find a better solution to what I do, but I don't see anything.  My solution isn't ideal by any means, but it works.  I create my invoice with 100% of the billed amount.  Then I add item discount and enter 10% (or whatever the retainage is).  I send that invoice to my customer. Then I delete the retainage discount line for my records so it back to billed at 100%.  When the payout comes, I apply to the invoice and it will show that 10% balance until it is paid.  There is no remembering to move the retainage from different accounts which is a big deal when you wait a year or more for the final payment.  It would be spectacular if someone had a better way.