@[member="Darth Shadow"]
It's really fairly simple. Personally, I used to play a great deal of EVE Online. So at some point, I just got used to it. In that game, they center a spherical grid over your spaceship. Ally and enemy targets are represented on the grid with the assistance of lines showing elevation and spheres showing you every ship's position in relation to each other. In addition, all hostile and friendly targets are listed off to the side in order of distance from your position.
http://farm1.staticflickr.com/74/201846640_0589ed8cf3_o.png
http://static.gamespot.com/uploads/original/416/4161502/2387761-0005.png
On a hex based grid, you can very easily do the same thing. The basic grid is considered zero elevation. Your movement along the X and Y axis is shown by normal movement along the existing grid. Movement along the Y axis (be it up or down) is shown by green numbers (moving up) and red numbers (moving down). Idealy, the maximum movement you can move (up or down) would either be 10 in either direction (for a map that is 20 x 20 x 21), or 20 in either direction (for a map that is 20 x 20 x 41). On this map, each level of elevation of declination from the target is considered one additional hex of distance between yourself and your target.
For example, a ship that is at 11/05(
5) is targeting a ship that is at 08/06(
2). The distance from one target to the other is 3 (for horizontal distance) plus 7 (for vertical distance). The horizontal distance is measured starting at the first adjacent hex and ending ON the hex that the target occupies. The vertical distance is measured starting at the first hex above or below the firing vessel and ending at the elevation that the target vessel occupies. The Zero elevation plane is included in this measurement.