I've seen Chevy Duty,
www.chevyduty.com, offering a driver's side battery tray just like what came from the factory. I've been thinking about this for my Suburban, as well.
I would just run a large gauge wire between the two batteries. I am thinking double ought gauge (00). I had another truck and had an isolator from a boat, which was really cool, but I never used it. You could run one and charge the other, run both, completely turn them off so no one could start (steal) the truck, etc. I would definitely use Optima red tops--they are the best: no doubt about it. you can even mount those bad boys upside down, no venting, spillage and they're tough as leather.
Good luck with your project!