Ok, JSGME should be in the Silent Hunter III Program folder, then double click on JSGME.exe to create the MODS folder. In the MODS folder you put all your EXTRACTED mods. If you are using GWX this has been done for you.
Then double click on JSGME.exe to open the mods window, your mods will be listed on the left and to activate them, highlight them and click the button called 'active mod'. When it's activated the mod will appear on the right side of the window.
The only other reason for your mods not to work is because you have the folder structure wrong. See this pic and pay special attention to the left hand expanded list.
