Hey,
1) No, the files need to be placed alongside the .exe as they are injected into it, so no separate folders. So all the files need to be dropped into the "Bin" folder. Remember to disable various third party programs that also inject into the games, Afterburner, some recording apps, D3D etc. they can crash the game.
Ok. Easy.
2) Yes, you need to disable FXAA for the best result, see http://www.neogaf.com/forum/showpost.php?p=44913691&postcount=655 - FXAALevel="0" is the important bit.
So in general (for any game X), disable in game AA either through the options or editing the files, I think that makes sense. Okay.
3) Nothing will work, you need compatibility / AA flags for the various options to have an effect and there's no flags available at present.
Not understanding this one as much. I'm thinking this would be the best probable settings to leave in the NV Control panel.

Also, you need to be running DX9 for it to work.
For this game or any game? I know my card supports 11.1 (supposedly). Is running the game in DX9 an in game option or something you select in some other fashion?
^ That's kind of an ugly post :/