I usually follow another method:
- I extract/install JSGME wherever I want,
- then I create a shortcut of its executable and I place it in the main SH5 folder,
- I right click on the shortcut and in the 'Start in' field (under 'Shortcut' window, see image below) I type the path to sh5.exe. In my case: "C:\Ubisoft\Silent Hunter 5"
- The first time I doubleclick on the shortcut, it will create a MODS subfolder in the same folder as specified in the previous step
following the steps from 2 to 4, JSGME can be configured to work with any other game, without having to install/extract it again for each new game