Sorry bud, I missed your reply for a few days there.
What I used to do couldn't really be called a 'Multiple install' i guess. I patched the vanilla game up to 1.2 and made back ups of the data folder, loaded various mods into the various back ups and just swapped them in and out at will. i think before I uninstalled the game a few months ago I was using Jonesoft's mod enabler for some stuff as well.
It might have got more complicated than that after Bi came out, I don't remember I'm afraid.
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