Hi Clive:
Generally speaking, one would set the flattens for the airport areas where AI traffic and/or ground support vehicle traffic will be displayed, all at the
same Altitude, as such traffic objects require a "flat" and un-interrupted surface over which to travel ...so they don't get "stuck" when moved by the AI traffic part of the FS rendering engine.
If you are uncertain as to where those 'traffic' areas may be, you can go into top-down view over the aprons, taxiway and user-aircraft traffic areas with the sliders for such traffic maxed, then run FS in the highest simulation speed mode to observe in a time-lapse, where AI / ground support traffic is going to be seen during a sample day.
It is probably best to make the flatten for such "traffic" areas as a 1-piece large flatten polygon, and set its Altitude / elevation at the
same value in Feet or Meters ...as the Airport Reference Point (aka "ARP") and Runways.
Surrounding flattens for a multi-level airport can of course be at 'differing' Altitudes if they do
not require a continuous level ground surface for continuity of traffic between those areas and a main airport traffic activity area.
FYI: Taxiways / Aprons will be automatically be rendered at the same Altitude as assigned to the "ARP".
If you by any chance intend to detail the changing elevations of the Aare river and the several nearby streams / canals etc., you may wish to use the Hydro polygon type which allows assigned Altitudes for each vertex point of the water polys (rather than the "mesh-clinging" type of hydro poly), so that they will cut down through the terrain as needed for plotting an accurate course relative to the nearby terrain and the airport ground level itself.
Google Earth in a '3D mode' tilted terrain view (even with its lower-resolution terrain mesh) will help with pre-visualizing the terrain nearby to Bern airport.
https://en.wikipedia.org/wiki/Bern#Geography
PS: If you opt to use the custom photo-real aerial imagery to provide textures for the airport surface
rather than
ex: a textured Ground Polygon / G-Poly, the attribute for the terrain surface may need to be changed to eliminate the "ground-roll" bumpiness and dirt or dust effect around the wheels of aircraft and/or traffic vehicles; this can be done via the 'Apron to SurfaceType converter' in Arno's ModelConverterX (aka "MCX").
http://www.fsdeveloper.com/wiki/index.php?title=ModelConverterX#XML_Apron_to_SurfaceType_converter
Hope this helps a bit more !
GaryGB