The PEQ function is only really used to eliminate a single large peak, (caused by a room mode) be it a wide-band peak, or a very narrow-band peak.
In order to make use of the PEQ function, you really need to have a microphone at your listening position to measure the sub's frequencies from 20Hz to the crossover point, (roughly 55Hz in your case) and then use the PEQ function to to bring down the largest peak. (It cannot be used to bring up dips caused by the room)
Without equipment, it's best to leave it disabled. (REW,(free) a Dayton iMM-6 with (~$25) a cheap microphone stand and 3' headphone extension cord is the cheapest gear and works well.)
As for basic sub set up, without measurement gear, leave phase at 0 and set the roll off to ~55-60Hz, then slowly adjust the volume until the subwoofer starts to become noticeable, (louder than the speaker) then turn it back down to where it no longer stands out. After that, turn the phase to 180. If it sounds identical, set the phase to 90, otherwise, just set it to which ever phase that sounds best from your listening position.
