Which game version do you have? In the latest one (1.16 and 1.02 for Entrenchment) there is a 'GalaxyForge' folder in the game's appdata directory.
Vista:
C:\Users\YOUR_USERNAME\AppData\Local\Ironclad Games\Sins of a Solar Empire\
XP:
C:\Documents and Settings\YOUR_USERNAME\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\
Put them there and they will show in-game as 'custom maps' (click the button small/medium/large maps).
