Questions about subwoofer phase

sub phase only affects the interaction between the sub(s) and speakers.  when the speakers and subs are in-phase they work together.  when they are out-of-phase they cancel each other. 

if you have rear deck speakers and trunk subs, the subs are distorting the rear speakers by moving the cones.  you want to build enclosures around the rear deck speakers to protect them from the sub pressure.  that would likely resolve the clarity issue and allow you to choose the setting with louder bass.

also, what is the HPF on the rear speakers set at?