I spent years making maps of the Trek (TOS) universe. I decided that trying to match most Trek locations with known stars was futile, as the Trek writers seemed to have completely ignored astronomical reality. Therefore, I decided that most systems named in TOS were too far away to worry about in my maps, which most concerned themselves with "core" regions. I used HIPPARCOS data from Winchell Chung's website and plotted habitable stars with galactic coordinates, with the z-axis indicated by color.
In this map of the early post–Romulan War era ( http://masazaki.deviantart.com/art/U...2170-369381515
), I've used real star names (sometimes non-Western ones) for some stars and assigned names, both Trek names and names of my own choice/invention, to stars without real names. Lines indicate commonly travelled routes, which are usually only a few parsecs, given the slow ships of the era.
Any star map eventually has to deal with the third dimension somehow (either by ignoring it or by indicating it), but once you get beyond a certain size, the third dimension becomes unmanageable.