2 more post since I started typing. I'm getting slow...
I've never installed LSH, so I'm unsure if there is an uninstall.
If you simply copied your SH3 directory that you installed SH3 to, no it will not install, as per HW3's comment.
There is a program that does all this for you. I forget the name...
What I did was ( and would suggest, if you have the hard drive space ):
1: Install SH3.
2: Make a copy of the install directory (Ctrl-C, then CTRL-V, windows will usually name it "Copy of [original folder name]")
(example: C:\Ubisoft\SilentHunterIII).
3: Name the copy 'SH3-original' or 'SH3-Unmodded'. (path would then be: C:\Ubisoft\SH3-original)
4: Install LSH, or GWX, (or any other) to the install directory: C:\Ubisoft\SilentHunterIII
5: Rename it to "SH3-***". *** would be "GWX" or "LSH".
6: Copy your "SH3-Original" and rename it, "SilentHunterIII". (install directory)
Then repeat steps 4 and 5 for each additional "mega-mod".
Add shortcuts named SH3 GWX and/or SH3 LSH.
Optional: You could then install SH3Commander for each install, just point it to the correct directory, hence the renaming of the files. ( and name the shortcut SH3 Commander GWX, or SH3 Commander LSH, then just click the one you want.)
Optional: You can then repeat step 6, if you wanted to have an original to make your own mods from.
You would never have to worry about "contaminating" your original files, because you know that "SH3-Original" is the backup.
If you need me to clarify, just let me know.
Barracuda