Open up My Documents\My Games\GC2TwilightArnor\Prefs.ini
Scroll down to [Game Options]
Change EnableMods=0 to EnableMods=1
Look for ModsDir= and enter the path to the mod directory you want to use e.g. C:\Documents and Settings\Blah\My Documents\My Games\GC2TwilightArnor\Mods\SWFix_Mod
Save the file and you should be sorted.