Looking at a number of dungeons in the creation kit there are a lot of black planes above the actual dungeon areas. What are all these for? The black color faces up they are invisible from below so they are not blocking holes in the ceilings. Just curious.

IIRC, I think they're to hide them on the map... I think.

If you place them 'above' your objects in the cell, they hide what is below them on the local map.

You can also script them to be 'disabled' once the secret door is found and opened, so that area will now show up on the local map.

...and for faking holes.

Hmm I didn't know that, thanks. Always thought they were for hinding the default cell lighting (mesh holes) for holes in ceilings etc.