I assume that if I am smoking for 2 hours that I will place 6 wood pucks in the tube then place the 3 bubba pucks on top, set the smoke time for 2 hours, and the last bubba puck will push the last spent puck off the burner? is this correct?
yes.
I would set the smoking part for 3 hours so you give the generator time to push 1 hour (3) of bubba pucks threw.
May want to increase the time to pre-warm the burner too.