Hi Haf, hohoho merry christmas etc.
you've guessed right on most of this, you have common sense after all
Level is indeed volume-ish
Auto on off etc determines if you switch it on or off or the sub goes to standby when not receiving a signal and on when doing so.
Cut off sets the maximum frequency signal that the sub will reproduce. A simple default setting is to look at the lowest frequency your surrounds will reproduce effectively and set it about 5-10hz above that, thus ensuring a smooth transfer from speakers to sub. Your amp will also have a setting for this I'm sure so why not match them?
Phase is trickier to explain, search the sub forum for a really good explanation. In the meantime, have a listen to your system with it set all the way to one side or t'other then listen again with it set halfway and let me know if you notice a difference. Some subs you do, some you just wonder if the knobs attached to anything. Much like some of my managers.
HTH
Bill