The only reason the AutoSaves load is because they're in the office, and no ship 3D artwork is drawn. The ones outside of the office have multiple changes.
The use of
MultiSH4 will help in any attempt to do multiple "installs", or run multiple copies of SH4 for mods. Remember, when you install the game, it creates a Save folder for itself, which is ~usually~ found at "C:\Users \YourName \My Documents \SH4" or similar, dependent upon the OS you are using. No matter what you do, it always will use that folder. Go through the documentation with MultiSH4, and see if you can get the hang of what is in that. You could also try looking through Rockin Robbins' package
Silent Hunter 4 Corruption Management System (SH4CMS). It does only work with SH4 v1.5 though.
Once SH4 installs, Windows has all of the C++ library stuff it needs, and all of the Registry settings it needs. Therefore, you can have a Stock install, a copy of the Stock install, but with TMO activated, and a Save folder for it (TMO is popular), another with Fall of the Rising Sun Ultimate (I use FRS for that Save folder), etc., and then don't have to worry about mixing up your Save files. Of course, each install takes over 5 gig of hard drive space, plus the Saves...
