I would treat them as a road or other imperveous surfaces.

I am assuming you are using GIS or finite element methods in modeling the drainage system. Best way is to represent the buildings and other hard surfaces as effective impervious cover (EIA). This is different from Total Impervious Area as it accounts for contribution to stormwater. Remember, these impervious areas are important as sources of accumulated runoff.

Thank you William and Timothy. Your suggestions are helpful.