The JSGME files go into the main SH3 folder. That's in steamapps/common.
Don't put the entire JSGME folder in there. Open it, and put everything you find inside it, into steamapps/common/silent hunter 3. The files you put in the SH3 folder are the JSGME program files and the MODS folder. So you should have:
steamapps/common/silent hunter 3/MODS
steamapps/common/silent hunter 3/jsgme.exe
and so on. There are a few more files but I can't remember their names right now. If your version of JSGME didn't come with a MODS folder, you can just make one yourself.
Make a shortcut of jsgme.exe to your desktop. Put your mods inside the MODS folder as in my previous post. Then run JSGME from your desktop and enable the mods. The mods are not going to work until you enable them in JSGME.
Also, when disabling mods always disable them in order. If you pick a mod from the middle of your mod list and disable it, you'll mess up your install. If that happens, just disable all your mods and enable them again.
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