The thing to do is to use
JonesSoft Generic Mod Enabler, aka: JSGME to "install" your mods with. Just pay attention to the Mod's folder structure as you "unpack" them on your hard drive. You'll want the Mod's folder, and directly below it the Data folder that holds all the info for the Mod. If you use JSGME and run it the first time, it will create a folder named MODS in your Silent Hunter game folder, and that's the place to put the actual Mod folder... MODS Mods...
example:
C:\Ubisoft\Silent Hunter WotP\MODS\Game Fixes Only v1.1\Data
The "MODS" folder is what JSGME creates, the folders after that are part of the Webster's_GFO_Mod_v1.1 download, that you pulled the "Game Fixes Only v1.1" folder (with all of its subfolders) out of and put into the MODS folder.
Also, before you start enabling mods, use the little blue "Tasks" link in the middle of the JSGME task, and choose "Generate snapshot of game files". It'll take a bit to run, but it will then have a list of all the original files prior to your putting extra stuff in there.
Be sure and read some of the "stickie" threads at the top of the forum list here, but especially THEBERBSTER's
Tutorials, How to do it, info... thread.
.