First off........
Welcome to SubSim!!
To make sure you have everything right, you'll need to open Windows Explorer and find your main "Silent Hunter Wolves of the Pacific" game files. It depends on the Operating System that your using, but on an WinXP system you'll usually find it under "Program Files/UbiSoft/".
This "main" game folder is where you'll find your JSGME files.
The "JSGME" execution icon and the "MODS" folder are just a couple of new files added to the Silent Hunter Wolves of the Pacific folder through the proper installing of JSGME. Your folder could look different, but the proper placement idea should be the same.
Open the "MODS" folder and you should find the folder "3000 Yard Bearing Tool (XXXXx)" there. Make sure you have downloaded the correct version for the resolution you use to display the game (the "XXXXx" could be "1024x" if you're displaying a 1024x game resolution). Open this folder and you should see three other folders......"Data/Menu/Submarine", each containing files or additional folders. If your folder structure looks like I've describe, you should be good to go.
Again, the folder structure should be:
UbiSoft/Silent Hunter Wolves of the Pacific/MODS/3000 Yard Bearing Tool (XXXXx)/Data/.........