The ductwork in my basement took alot head spaces, but it just merely sit above the top frame of the door, so my ceiling panel is closely attached to the ductwork pipe. In certain places you may place a frame around the ductwork so that you can attach roofing panel to it.
Here is a very good guide for finishing basement, you may refer to the topics on framing ductwork.
http://www.howdididoit.com/Basement/