There are two ways to connect ductwork between floors of a building.
Floors on the Same Drawing
If your floors are all in the same drawing, draw your vertical duct on each floor and connect them with a duct. Query the connecting duct and set the graphics to Transparent. That will keep the air flowing between the floors, but not actually draft anything. If you use our pressure drop calcs, set the pressure drop in the section to 0.
Floors on Different Drawings
If your floors are on different drawings, use the DM HVAC->Duct Centerlines->Insert Drawing to Drawing Connection command. It will connect two drawings for you.