The maps are in the install directory. For steam it's in your steamapp directory.

Note if you want to edit existing maps, you should not change these default map files. It might keep you from playing multiplayer. Rather, make a copy, paste it into the GalaxyForge folder that's in the Rebellion "My Games" folder.

Do you want the location of the maps that come with the game, or the custom maps directory?

Copy the maps you want to customize to 
C:\Users\[username]\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\GalaxyForge
for Vista\7

Stock maps
Do not change the stock maps, or anything in the insatall directory 

32bit
C:\Program Files\Steam\steamapps\common\sins of a solar empire rebellion\Galaxy

64bit
C:\Program Files (x86)\Steam\steamapps\common\sins of a solar empire rebellion\Galaxy