Calling all stereo Gurus

I'm about to upgrade the stock stereo system in my new Mastercraft and need some advice from the high end stereo junkies.. Boat is an X-45, equipment is as follows...

Stock mids/highs, only upgrading the subs for now.

I'm planning to install the following:
(2) JL Audio Slash 1000/1 amps
(2) JL Audio 13W7 subs in a custom box made for the compartment under the observer seat.
(1) Kinetik 600 installed as a capacitor

My questions include....How can I stabilize the power supply system and batteries so that it wont drain my batteries? What all must I do to allow the system to be played for extended times with the engine off? More Batteries? How should I wire them? My current setup has one starting battery, one battery for the accessories. The alternator charges both, even while the switch is on battery #1 (starter). Also, I'm wondering what is the best way to keep these amps cool? Should I install a few fans to blow on the amps since this is going to be in a closed location. I will vent the area when I'm not running by opening one of the seats. So, for you guys who know your stuff, how would you set this equipment up?

Thanks!