Your assessment is correct in that you can't have a room inside a room. So you need to think about why you need the area of the entire open space instead of each individual cubicle. The sum of the cubicles plus the space around them will still produce the same totals and the same percentage allocations if they are classified the same as the single large room. Your purpose or intent in tracking the space should define how you want to model or describe it.
There is a different way to do both that might be useful. You could do the individual "rooms" for the cubicles and the enclosing open area as another room. Then you can use a "zone" as a handle to group the cubicles and enclosing space together. That is, "zones" are collections of "spaces."
If you are concerned with the amount of effort to model the cubicles, consider creating a Revit family. You may need to use a room defining boundary in the family.
Mark Evans
Mark Evans
Senior Product Manager
AEC Division, Simulation Product Line
Autodesk, Inc.