[Suicide Junkie]

well, if you look at the galaxy, its mostly flat anyways.

You could use the map editor to make a multi-level map.

If you want a system directly above some other one, just place it one square away.

You could have systems:

.....A...W
X.....B.....Y
..Z...C.....

Pretend A,B & C are above each other in space.
A connects to B, B connects to C.
B connects to WXY &Z.