Why do we have 2 copies of the game?

That bothers me from the start....on example we cleared cache files in CLOD version which is installed in my docs. Also earlier in the patching process we changed conf.ini values there. Now with latest hotfix we need to copy that into steam/steaps/common/clod. Like last two beta patches.
So whats up with two versions of the same game? Which conf.ini should be changed to affect the game etc? One from the my doc or from steam?