where did you put the folders

Vista:
C:\Users\username\AppData\Local\Ironclad Games\Sins of a Solar Empire\

XP:
C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire\

Ok, if you are going to play them in original sins, put the mods into 1.16 folder. If you are going to play in entrenchment, put in 1.02 folder.

Please note these directories may be Hidden by default. To unhide them, go to your Control Panel -> Folder Options -> View and set yourself to view hidden files and folders

to enable them, go into the game (either), go to options, then go to mods, last option on the menu of options, select the mod you want to use, and then click enable. If you have entrenchment, you can enable mutliple mods, but if they contradic each other