Follow SMACNA strategies for HVAC protection that are appropriate to your project. These include items such as the following:

wrapping ductwork and or ventilation equipment in plastic once it arrives on site;
ordering ductwork pre-wrapped in plastic before it is delivered to the site;
placing ductwork or ventilation equipment in a room away from construction work to protect it from dust until it is installed and covered;
covering exposed grilles with plastic once ductwork is installed;
and laying plastic over underfloor air systems to keep out construction debris.