I think your only option for the stairs would be to box them in. Since your soffit is going to be back there anyway, you could hide it behind your soffit. This is no BIG sketch, but maybe it will clarify what I'm thinking.
If you are thinking of a sloped ceiling there, I would probably contact Ted and run it by him.
Also, how long are your supply and return ducts? Keep in mind that a 90 degree bend adds an equivalent length of 30 pipe diameters (IIRC). So each 90 degree bend would be like adding an additional 13' to your run for a 5" duct. I think the general recommendation is not to exceed 25' of duct length, but there is al to that goes into sizing those things.
EDIT: I'm not sure why the image is rotated like that. It's not like that in my photo bucket account?