The BEST place for duct work is inside of the thermal envelope (the insulation layer). This will save you a lot of energy.
A typical solution in flat roof houses is to have a lower section of ceiling, called a dropped ceiling. Usually this dropped ceiling area is above the hallways, bathrooms and closets.
It is also possible to run the duct work in soffits at the edge of a room. A soffit is a drywall box around the duct work. This hides the duct work, but creates a bump out at the top of the wall that may not fit with the style of your house.
Another alternative is to expose the duct work and have it be a feature of your house. Work with your architect or designer and tell them that you want the duct work in the thermal envelop.
DO NOT settle for duct work on the roof. That's throwing money into the air!
For more information:
Read Erik Henry's Q&A "Do we still need ductwork in a passive home?"