M14, looks right matey.
Just be sure that when you install mods, they look like this:
C:\Progam Files\Ubisoft\SHIII\MODS\mod-folder-name\mod files
(right)
and not;
C:\Progam Files\Ubisoft\SHIII\MODS\mod-folder-name\mod-folder-name\mod files
(wrong)
Once you place your mod in the folder in the above correct format, start JSGME, look down the list on the left of the screen, select the mod you want from that list by left clicking it to highlight, click the right arrow so it is added to the right hand list, and your mod is enabled.
Semi-transparent folders are just those that are hidden by default. You won't need them anyway
Just assume they're doing their job.
::Edit - sorry if I'm repeating anything you know already, I just saw your other thread. Don't mean to come off patronising.