oh.. i'm sorry. you mean your wow key bindings and settings. ooohhh

then, yes.. you may need to have multiple directories if you are going to have different key bindings.

when wow saves the data, it is saved into the config file. then when you go into the other wow, when you change those bindings and save, the file you wrote the first time will get overrun.

wow wasn't designed to be run as multiboxing.. so some things, like key bindings, might get overwritten