If you are running the latest patch (Sins 1.16 and Entrenchment 1.02) you need to put the custom maps in the Galaxy Forge folder. For Windos XP it is the file name below. It's a hidden folder, so just do a search (you can just search "GalaxyForge" and it will find it) and have it look in hidden folders. I just made a shortcut to the folder on my desktop once I'd found it.
"C:\Documents and Settings\user name\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\GalaxyForge"
Hope this helps.