If everything is wired correctly then yes leave the phase shift as it is. You'd soon know if you have something out of phase because you would lose most of your bass and the system would be uncomfortable to listen to for extended periods.
I used to have a subwoofer with two 12" drivers that pointed inwards at each other, in that instance the two speakers HAD to be run out of phase with each other for the box to work as designed. That's just an example of when you would want to use phase switching.