fireftr18 has the right of it. However, there is another way to do it also. First, uninstall then reinstall SH4 and leave it separate this time.
Now, you need a small utility called
MultiSH4. This allows you to make separate installs for each mod which eliminates the mod soup that fireftr18 was talking about.
What you do is this:
1. Create two separate folders. Label one OM and the other TMO
2. Copy the original game files from the SH4 folder into each of the two folders (OM and TMO).
3. Load the JSGME and MultiSH4 into each of the folders.
4. Use MultiSH4 to create save folders for each OM and TMO.
What MultiSH4 does is create a save folder for each mod in your My Documents folder. That way they are totally separate and you won't get the mod soup with which your struggling now.