Normally, all the outside walls are assumed to be exposed to the outside ambient air. Alternatively, surface connections in CFAST can be used so that a fraction of the outside wall, ceiling, or floor in one compartment is connected to the outside wall, floor, or ceiling of another compartment. Energy can then be transferred from one compartment to another by conduction. Unless your surfaces are highly conductive (such as metal surfaces on a ship), there would be little difference in the results.
CFAST (and all zone models) treat compartments as rectangular parallelepipeds. To model other shapes, you need to define a compartment with an equivalent surface area (for heat transfer) and volume, keeping the ceiling height constant (for smoke filling). See an example of using complex geometries on page A-10 or this document:
Richard Peacock