You will still be able to play out of one folder. The only difference would be when you log in and have to select which account in the drop down. The only benefit of having multiple folders or symlinked folders is different config files so that it can remember your previous choices.
Also if you are using IS then you dont have to worry about multiple folders either since I believe it houses it's own config files. Someone can correct me if I am wrong there. Haven't jumped into that yet.