Your mapping would also depend on how you handle FTL travel. Is it like Star Trek and Star Wars where you just warp from wherever you are, or are there nodes like in Wing Commander and Babylon 5? Another thought to go with the idea suggested by Ryan K, perhaps have distances from the standard plane of reference depicted by two separate colors to show how far up or down from the plane they are. You could go further by adjusting the shade. I don't know how well it would look once done though.