I too am concerned about the "helper". I am not 100% sure I am getting through to the contractor on the importance of sealing the existing ducts.
We don't have any flex duct connections - all take-offs are galvanized hard metal duct and main trunks are rectangular metal (all presently covered with duct insulation).
I am doing the register boxes myself - on the inside as far as I can reach in. But I have been using mastic "putty" to plug openings and aluminum foil tape (Reflectix) over joints. I will try and pick up some paint on mastic (hard to find here) and some mastic backed tape - I think I saw that somewhere here.