I have 1 DAoC folder that has the original, the other server and Phoenix.
If you execute the Phoenix.exe it will patch files that are unique for Phoenix, so you won't log into the other server. When you want to play in the other server, when you run it's .exe it will patch again to amend the files to their server needs.
So you don't have to worry about logging into Phoenix and suddenly be over there, each server has different settings.