No, it would literally be your window's game object. Generally the UI is organized into windows -- which is just a game object under which you place your widgets. For example, for a main menu you'd create a game object called "Main Menu", and put everything related to the main menu -- labels, sprites, etc -- as children of this game object. So in order to show or hide this window you'd use NGUITools.SetActive.
There is no need to have more than one UIRoot in your scene.