Ceilings are by default "Bounding Elements", so Spaces will stop at the Ceiling no matter what the Upper Limit parameter is set to for the Space.
If you are not looking to have separate Spaces for your plenums, then the easiest process is to adjust the Bounding status of the Ceilings in the Architectural model. Here's how you do it.
* Open the Architectural Model.
* Open, or create if needed, a 3D view that contains the entire building.
* Switch to the Wireframe Model Graphics Style.
* Do a crossing window to select all elements in the model.
* Filter for just the Ceiling Elements.
* Alt+Enter to go to Element Properties.
* Uncheck the "Room Bounding" Parameter.
When you re-load the MEP model, the Space Geometry should not react to the Ceiling Elements. Now if you get a new copy of the Architect's model, you will need to re-do this process, but it is still the path of least resistance to accomplish the task.
A handy way to validate this is to use the Heating and Cooling Loads dialog, as this allows for the visualization of the Space geometry.
Hope that Helps,
Kyle B
Revit MEP Product Manager
inside-the-system.typepad.com
Kyle Bernhardt
Director
Building Design Strategy
Autodesk, Inc.