You should mount the battery close to the amps, I had an Optima behind the wall of the storage compartment between the cooler and the hull. I mounted a group 24 battery box minus lid to the back side of the bulkhead to the left side of the storage compartment when you are looking in the door. I mounted a Hellroaring isolator/combiner to that panel as well, that would connect/disconnect the second battery when charge was applied either via the alternator or my onboard charger. All that crap is going in the SX, since I'm gonna take a bath on the E22, I pulled all that stuff off. There are pics on one of the original maintenance docs I put up.
If I were to do it from scratch (Cal:) I would use a Stinger 200 amp continuous duty solenoid, it would energize when the boat is running and connect the second battery + terminal to the charge source. The power and ground run straight to the amps, short run with big wire. This is a cheap and efficient way to isolate your second battery. It is a relatively short wire run from the Perko to the storage compartment.
JL is a good choice for the amps, I am going to use Old School Zed Audio made Planet Audio amps for my systems. I have cornered the Ebay market on them, got some real deals so far. I'm going to disassemble them and have the extrusion (amp cases) anodized purple to match the purple LEDs I'm putting in. Cal, with all your big time pimpin' you definitely need to put LEDs in your boat. It is easy and pretty cheap, lots of bang for the buck. I am also going to run 8 interior speakers off one 600 watt two channel amp at 2 ohms/channel There is no reason to go to a four channel when two will do.
I mounted my amps in the storage compartment on the hull side. I glued MDF blocks to the hull and screwed panels made from cheap ass cutting boards (home depot) that I covered with matching cheap ass grey marine carpet from Lowes. On the SX it looks like two of my amps will fit on the wall on the left side of the storage compt, the sub amp will go on the hull in front of the rear Vdrive storage compt.
Here's a pic of the amp install on my E22. I put a homemade LED cluster on the underside of each amp mounding board so they glow from underneath at night. More crap like that coming for the SX:) You can make your own LED clusters if you are a cheap SOB like me:) These amps are staying in the E22, it is at the boat dealer for sale right now, CHEAP:) Good deal for someone!