Sorry my explanations leave alot to be desired I know..........yes I did point it to C/Program files/Ubisoft/SilentHunterIII and had the correct folders appear, but when I put the mods into the mod folder, it would look like for example the Tonnage one would have a folder called NYGM Tonnage War v2.0, inside that I'd have folders "data" and "documentation" what I did was ran JSGME and it would have the NYGM Tonnage War v2.0 folder on the left hand side, so I'd then tell JSGME to install but what I found was that instead of installing it would simply put those folders in the main SH3 directory.
I hope that better explains my miserable attempts, I did manually install it successfully once I gave up on JSGME, having said that I'd prefer to use the JSGME as it is not as long-winded as manually!!! lol
BlueGlow