The second copy is really easy since I don't play that copy so to speak.
In the Microsoft games folder I create a new folder I call "MFS backup", then I copy ALL of the FS9 folder contents into that backup folder after I do a CLEAN install. Then I can mod the installed MFS all I want.
On some of the games I have I wait to copy the "installed" folder contents until after I have patched and changed the video card settings and controller configs... but it depends on if I am going to "tweak" them to a semi unstable state or not.
In fact I think I have three folders for CounterStrike Source :) and I can't tell you how many times I have used the copy and paste on Stalker ;)