That, I'd say, would depend on how deep most of the main tunnels are -- tunnels in the Underempire would be similar to waterways in most civilizations with commerce centralizing around it.
This is just guesswork, but I feel like depth underground would go hand-in-hand with a skaven's rank and station in skaven society. It's either in one of Thanquol's appearances in the Gotrek & Felix books or in his own books, but at one point Thanquol is punished by being put into a large chamber where the roof had been decorated by the dwarfs with gems to simulate the night sky and its effect is torturous to the skaven psyche. This leads me to the thought that those with power (and items of importance) would be as far down from those terrible open spaces above as possible and kinda twists the lead from behind approach into lead from below when concerning their civilization.