As example, here is a map of the planes I made for D&D/Pathfinder (see attached file).
How do you tackle things like this? Share examples if you like.
Mapping 3d objects has been a big challenge for me due to the nature of my current setting. I've found though that heavy use of abstraction and/or top-down projections can help at least get a rough sense of the layout. For more intricate stuff though (like say the map of a dungeon with multiple levels) it really needs to be broken into multiple sub-maps.
As an example of the first one though you can take a look at one of my maps here:
(http://fc03.deviantart.net/fs70/i/2012/042/c/d/the_expanse_by_garrettdmorrison-d4pbvn0.png)
This being a 2d projection of a 3d space it's of course not fully correct but I still think doing a map in this style will probably serve you well for gaming at the table. It at least lets the players, at a glance, know roughly where everything is located relationally to everything else (is it close? is it far away? is it across the map? etc).
One thing I appreciate about your specific design, Fortunato, is that it's similar to what actual ancient humans would have done to represent such ideas. Part of the fun of such a representation is trying to figure it out, and having it explained to you by a wizened old sage.
I've actually used 3D software to help me depict the diagram of the planes for settings as well, though I've only done this once, so have no other examples on how I'd do it. I've never needed a diagram of the planes before, but since my setting is unique and has a different planar construction than typical D&D settings, I thought I'd include this with my published setting.
The Wheel of Life planar construct:
(http://www.gamer-printshop.com/kaidan/wheel-of-life-construct.jpg)
I like how the Nobility sits next door to Yomi; very fitting given their portrayal. The rice shoots planted on the Commoner sphere are another nice touch. It took me a while to spot the skull on the Tainted sphere though.