Answers below match to your bullets
- I would use the natural ventilation option in EnergyPlus's Zone Ventilation Design Flow Rate object
- You generally will at least want to add core and perimeter zoning, but may add more to represent different conditions in different areas or to break up very large spaces to represent different zone temperatures.
- If your can run EnergyPlus and see the sub-surfaces there, it is probably fine, but it should not be crashing in the 3d view in the OpenStudio Application. If you send the model to openstudio@nrel.gov we can try to replicate the crash and identify the issue with our 3d viewer.
