[Pisces]

You can reuse the executable of JSGME by using shortcuts. GWX 3 contains an older version of JSGME, and places the executable in the SH3 game base folder. But proper install procedure (for multiple games) would be to: (First read the documentation of the new version )

1: install JSGME_Setup.exe in any ordinary place for applications: Program Files is ok, as is C:\Apps\JSGME or whatever.
2: Once it has installed a JSGME.exe in there you make a short cut to it and place it wherever you find that convenient (Desktop, or game base-folder most likely). Include the name of the game you will mod. As you might get confused and use the wrong one when you will have more than one shortcut for JSGME.
3: Open the properties of the shortcut, go to the shortcut tab: Change the "Start in" path to point to the base-folder of the intended game you want to modify. Like C:\Games\SilentHunter3
3b: Leave the Target field as it is. Pointing to the place where the JSGME.exe was installed (I have it at: c:\Games\JSGME\JSGME.exe)
4: Press OK, or Accept and close to end the shortcut properties window.
5: Doubleclick the JSGME shortcut for the intended game. It should now prepare itself for first use and create a new MODS folder (if not already there) in the base folder of the game. The JSGME executable stays in the one spot you installed it in. And will not leave multiple copies in all your modified game base-folders.
6: Extract or copy your mods into the MODS folder in the game base folder as usual.
7: Start the JSGME shortcut for the game (or select it's still open window) again to enable the mods in the right order.