There are two ways to connect ductwork between floors of a building, depending upon whether the floors are on the same drawing or different drawings.
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 calculations, set the pressure drop in the section to 0.
Floors on Different Drawings
If your floors are on different drawings, use the Insert Drawing to Drawing Connection command to connect the drawings.
The Ductwork Across Multiple Floors section of the Design Master HVAC tutorial shows how the command is used.