thats not the problem and thats not what that setting is for...
the phase that is adjustable with that kind of setting is in relation to the other speakers, ie: if the subs are mounted backwards in the box to show off their super sweet magnets, you don't want the sound waves to be opposite of all of your other speakers and then canceling their sound out.
I'm talking about some of the sound waves that leave the speaker cone and go directly toward your head, then there are other sound waves that bounce off of other sh!t like the braces in the trunk, then bounce back and reflect off of the rear of the trunk that are now heading in the same direction as the original sound waves, depending on the distance the secondary set of waves have to travel, they could be out of phase of the primary sound waves and cancel them out...
with that in mind, if you throw the original sound wave off by (doesn't really matter but) lets say 180*, the secondary set of sound waves will still be delayed by the same amount of time so the end result will be the same no matter what you set the phase to. settings can't fix this, only placement and distances can. even a great DSP with time alignment can only correct speakers from interfering with each other, not with speakers interfering with themselves.
if that doesn't make sense, think of a muffler without any fiber stuffing or anything like that inside of it, it uses different chambers and different angles of metal inside to reflect sound in different ways so that the waves cancel (at least some of) themselves out without interfering too much with the flow of gases.