Sorry to say this, but the answer is, "It depends..."
It depends on what you want to accomplish with the data/model. If you are a obsessive about matching the BOMA or IFMA space standards, you would want to treat it to match them. That probably means you poly-line it at the floor of the atrium, classify it according to it's usage, and do nothing at the upper levels. I say probably because I unfortunately don't recall what the standards say and I don't have time to look it up. On the other hand, if you have "stuff" hanging in there at various levels, you may want to define a space at each floor so that you could place the hanging equipment and write work orders against it and have a location attached automatically. A little bizarre, but I could see it. I have also seen people poly-line the atrium at each floor because they compute their floor area based upon outside dimensions (instead of where there really is a floor) and want their area totals to match up.
So, no real clear answer, unless you are sticking to BOMA/IFMA.
Mark Evans
Mark Evans
Senior Product Manager
AEC Division, Simulation Product Line
Autodesk, Inc.