If you want my recommendation on the most accurate way to model an atrium like this in EnergyPlus (as of Feb 2022), you should model the atrium as a single Room and use the Air Flow Network. The spaces around the atrium can all be different Rooms and, if the Rooms are completely open to the atrium (without an interior wall or window or anything like that), then you can use an AirBoundary in between the surrounding Room and the atrium Room. The AFN will still account for buoyancy-driven flows from the lower floors to the upper floors through the atrium but EnergyPlus is just not capable of modeling sub-zone air temperature differences and the “Cannot Do” section of the E+ reference is very clear about this:
Air Boundaries in Legacy are very poor representations of virtual boundaries since they completely block all radiant heat exchange. So I don’t recommend using Legacy.