I would like to design a dungeon-like location, a city surrounding a keep built on a limestone hill littered with caves. Tunnels and caverns would connect certain city locations to keep dungeons but also to some natural formations, which are used as building parts, free storage space, or in some deeper cases unused, abandoned or unexplored. The whole structure has at least five levels, but unlike in premeditated multi-storey design, natural and organic cave formation does not follow a set of distinct, parallel "floors". And most importantly, I have to explain that network to players.
I'm looking for a good methodology of wholesome design and representation of a three-dimensional dungeon. It has to be representable on paper as a map (innovation welcome - folding paper structures?). It has to include non-sequential "levels" (e.g. ramps going through a level without accessing it or "half levels"). Is there any such methodology available to players, short of making a 3D model with Blender or something similar?
The map is supposed to help players realise which bits of the city are connected and what is required to travel underground. E.g. in Game of Thrones, you could travel by horse underground from the Red Keep dungeons to city docks. I want that fact to be immediately recognisable.