Clean and Modified Versions on Same Computer

This may be an unsophisticated question for the modders on this site, but is it advisable and/or possible to run multiple versions of BG:EE on your PC? My thought is that if I start modding a game, then this would make things difficult if I decided to do a multi-player game with someone with the vanilla version (or who just doesn't want to play with the same mods). I'm not sure how this could be done or if it is a good idea but would appreciate the thoughts of those who know this area better than I do. (i.e., everyone with something to contribute on modding!)