Phase varies the phase of the output signal. Normally it's just a 0, 180 two position switch. Like that it has the effect of reversing the polarity of the subs. Depending on the install, crossover freqs and midrange speakers, you may get a smoother midbass transition with the subs out of phase. If the phase setting is a variable dial, it will have a center freq associated with it and will adjust the phasing relative to that center freq acting as an analog time alignment filter.
A subsonic filter is usually employed to protect a sub from overexcursion by attenuating freqs below the cutoff freq. It is essentially a high pass filter set at a really low freq. If you are running a lot of power to a sub in a high tuned ported box, a SSF is a good insurance policy to limit the power going to the sub below the tuning freq where the air moving through the portis actually reinforcingthe movement of the cone and driving up excursion while cancelling out output.