In Floor Manager you invoice for the full desired amount then once the Invoice is created, a portion of the invoice can be moved to retainage as a separate step.

Click on the small arrow next to the word retainage and type in the desired amount of the invoice that is to be held in retainage.

Once this is completed, it moves a portion of the job into a retainage column on the Accounts Receivable Aging Report. 

When the Customer is ready to pay that portion > go back to the Invoice and enter a zero in the retention field then re-print the invoice.  This places the amount of the Retention in the balance owed area.