Here is the setup I am planning (already have all of the equipment).

Two batteries mounted up front with the gas tank.

One battery will be for the motor the other will be for the swamp lights, nav lights, stereo, and winch.

I plan to have a stereo amp and 2 bank onboard charger mounted in a passenger side box at the back of the boat.

Can I run the 2 batteries to a distribution block on the bow and just run a single power and ground to a distribution block at the stern, then branch off from there to the 2 bank charger, amp, and motor?

What size/type batteries do you recommend (Optima's are out of the question)?

I be all confuzud. say that again s l o w l y I think you are trying to push a 2 bank charger up a single circuit if I read u right. keep everything seperate EXCEPT use a tie switch that should remain open unless you kill one bank, then tie them together to get running and then seperate them again

X2. He got me all phucked up too.

If you mean running your batteries paralell and running a two bank charger "one to each battery" then yes you can but dc current doesnt work like ac so the longer the wires the more voltage drop you will have. so if you start running a motor/ battery cable from the front of the boat to the back you will need at least a 6 to 4 guage cable. battery chargers will do the same. if you run long lines from charger to battery you will need to up the wire size or you will be under charging your batteries. there is a formula for running dc wires but bigger is always better.

Put everything where you want it to be except the charger. I would keep the charger next to one of the batteries and then you can run an extension to the other battery if it's not close. I was a little confused on how you planned to wiring it with the distribution boxes but my suggestion is to keep the 2 battery curcuits separate. The only thing going to both would be the charger. That was a short in one won't short out both batteries.

Going to keep the most important battery (motor, bilge, running lights) in the back, by the box the charger and amp will be in. Second battery (for amp, winch, swamp lights) will be up front to even out some of the weight.

sounds like you got it figured out, one in front and one in back, tie both grounds together and put a heavy duty tie switch between them, just in case. this is a VERY GOOD INVESTMENT. tie em together w/ a # 6 minimum but I would use # 4 fine strand. just cut your hot and install tie switch. you will thank me later.