Two batt install?? Subs??

Hello, Im getting into the car audio scene, but now im uping my game and buying a new system. my everyday driver is a 99 Grand marquis. i plan on installing a 200/250 amp alt, also a two battery setup with either kinetik or Odyssey batteries. i have a pioneer deck, alpine 4channel ran to some infinity kappas two ways. i have three MRP-M1000 Alpine amps for my subs, the amplifires are 1000rms 2000max watts each. im haveing trouble decideing on Subs. i looked at re fi treo, with a large investment i want to make sure i get my $'s worth.  im thinking a 3 sub setup. also does anyone know of someone that makes a 2 battery install kit? thank you for your input         -joe