" double "SH3" folders in MyDocuments"
You don't want that. Multi-SH3 allows you to create a separate folder in My Documents for every install of SH3 on your system. You must give each of these new folders a different name that you will automatically associate with whichever copy of SH3 you are running at the moment.
Here's how you do multiple installs: - assumes you only have the one original SH3 install at this point AND that you've run the program at least once to establish the SH3 directory in My Documents.
1) Using the Uninstall program on the SH3 CD, remove the existing copy of SH3 from your system.
2) Manually delete the SH3 directory and all its contents in My Documents
3) run a registry cleaner like CCleaner.
4) using the SH3 CD, do a clean install of SH3 into c:/Program Files(x86)
DO NOT RUN SH3
5) Create a new directory on your c: drive - call it /Games
6) Within /Games, create as many new sub-directories as you want installs of SH3, plus a spare ('cause bad stuff happens). Name them whatever you want. I call mine SH3+GWX, SH3, and SH3 Virgin 1, SH3 Virgin 2, etc. The Virgin directories are spares 'cause $hit happens and I don't want to have to rip everything out to start over.
6) Into EACH of these new sub-directories, copy the root directory "Silent Hunter III" from c:/Program Files (x86)/Ubisoft. Do not rename these new root directory copies.
7) If you are going to use GWX, run the GWX.exe and install GWX into one or more of the new root directories created in (6).
DO NOT RUN
8) Copy MultiSH3.exe into all of those new root directories.
9) For each install of SH3 that you plan to actually use, RUN MultiSH3.exe from within that root directory to create the appropriately named sub-directory in My Documents. Each must have a different name. For example, my sub-directory for my copy of SH3 with GWX is named "GWX". My stock vanila copy of SH3 is named "SH3", which also happens to be the default.
10) You can use JSGME to install any desired mods onto GWX anytime, but I prefer to run my 1st career mission in my SH3 with GWX program before I do that, just to be sure my install works ok before I start modding it. I can always delete that career later. YMMV.
11) Copy the SH3.exe icon from each new install to your desktop, renaming each as soon as they're copied. You want to know which copy of SH3 you're starting up.
Good hunting.