When you install JSGME it creates the MOD folder within SH4.......then you have to take a snapshot of the stock game files with JSGME and then unzip and move the files into the mods folder,then install them via JSGME.
the link is the best "How TO Install MOD's" I have yet to come accross.
http://forums.ubi.com/eve/forums/a/t...5/m/5181035206