Go to "My Documents", then find a "My Games" folder. Go to "Ironclad Games", "Sins of a Solar Empire Rebellion". This is the main folder for things like saves, maps, mods, settings, basically the game files you want to mess with. Here there is a GalaxyForge folder. That's the one you put maps in.
Also, you use the GalaxyForge program from the main directory, not the one download from this website right? The one from this website is only for Diplomacy and earlier versions of Sins.