DJR@2013 MXZ

I bought a 2013 MXZ with upgraded wet sounds speakersj (All of them)..... how big a dif does it make to have that sub box vs. the 12" sub in the open under the drivers feet...? That custom box looks awesome!! Also, does it help to have more batteries.... I have the two stock ones that take up all the room in the storage compartment... Seems after a while the speakers kinda start giving a shredding sound like they are hungry for power... I have 4 large tower speakers and then all the ones in the stock spots Im not really a tech guy but know it can sound better than what it does... Any input you have will be appreciated...