Before getting down to the subwoofer phase setting, you need to clearly understand what a phase is.
Simply put, when a subwoofer and main speakers are in phase, the woofer cones on the subwoofer and speakers are synchronized during forwarding and backward movements at the subwoofer crossover frequency. This way, the output of each component is increased.
If the main speakers and subwoofer are out of phase, the woofer cones on the mains move forward, while a subwoofer cone performs a movement in the opposite direction. Thus, the output of each element degrades.
You may figure out that your subwoofer is out of phase listening to the audio produced. Phase cancellation is most evident in low-frequency sounds. Typically, you can hear a thin-sounding signal with little or no bass. Another clue is the kick drum, or bass guitar moved around the mix instead of coming from one spot.
However, while talking about a sub and main speakers being in/out of phase, we need to be accurate with the terms. Actually, such a synchronous movement is possible at one definite frequency. This happens because a phase of both elements is altered with frequency changes. If you bring them in balance at 90Hz, this may be of minor help at 120Hz.