With the simple mod manager JSGME I don't need any multiple installs of the game, I can remove all mods with a single click and revert to my initial install. JSGME is also able to install an entire modlist for you that you have saved previously.
I don't know which version of the game you have, SF doesn't tell me anything (Maybe StarForce copy-protection?), but what i know is: for most of the mods you are going to need the latest game upgrade which is SH4 U-Boat Missions v.1.5.
XS