If you have an active/active configuration and do Halt, partner will automatically takeover. If you intend to shut down both partners, use "Halt but dont get taken over" (or whatever it is called in GUI). Takeover state is persistent, meaning that when you switch filer(s) back on, they come up in the same takeover state.
Usually shutdown is pretty fast; to be on safe side, it is better to open console and wait for CFE prompt before physically powering off. If you open console anyway, you do not need GUI - just do "halt -f".