Just put all of the Project 1999 files in their own directory. On my machine, I used to have c:\p1999. Everything was in there. (now its on a flashdrive on my keychain, but that's another story
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If you want Live too, just install that to some different directory (i.e. c:\program files\sony\everquest - or wherever, as long as it is NOT the same place as Project 1999).
Your shortcuts for each game will have to be different as well. As long as you think of them as two completely different games (heh, which they are) you'll be fine.
EDIT - Bah, nilbog beat me by one minute, and with a clearer explanation too.