When you wish to invoice the left over retainage amount, you need to select the 'Retainage invoice' document type, rather than the 'invoice' type. This makes the entry behave a little differently. Essentially a retainage invoice will use all the standard fields as a regular invoice for the amounts, but you can't assign further retainage.

Are there particular fields you see on the retainage invoice that aren't printing on your specification as you expect them to?