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I would have recommended using the Construction:AirBoundary object, but from the Input Output Reference it says that a base surface with this construction assigned cannot contain fenestration (the diffusers). An alternative to the air boundary construction would be using a standard Construction object that is comprised of one material layer that is thin and won't block much heat transfer or store much heat. Either way, you will have two zones separated by this base surface containing the diffuser fenestration surfaces.

This will likely be faster and easier than your post-script idea of drawing rectangular prisms from the ceiling down to the diffusers, mainly because of the extra time to draw 5 base surfaces (4 walls, 1 "floor") for each diffuser instead of one base surface containing all diffusers. I will note that you do not need to split the roof surface for convexity issues. That applies to the outermost edges of the base surface only -- the addition of skylights in a roof surface make "holes" in the middle of the roof, but that doesn't change the convexity of the roof. This applies to the TDD domes drawn within the roof for either approach.