you put one in each game folder for each version you are using.
open the ubisoft folder (if it has one) and put jsgme inside the silent hunter folder.
(games installed other than in the default location may not have a ubisoft folder)
if you have dual installs do one for each install and what i do is put a shortcut on the desktop for each game version and the corresponding jsgme shortcut from each game folder and name the shortcuts "sh4 v1.5" or "sh4 v1.4" or "sh3" (i do the same for the mission editor as well)
this way its easy to see and quickly change what mods are active for each game version.
capt cox is no longer around so you wont be able to contact him but here are his mods:
http://www.subsim.com/radioroom/showthread.php?t=118341
i havent seen or heard about sober in a while so i dont know if he is still around or not.