audio system set up advice

[ECeptor]

Although my boats system is not wired/set-up properly, I don't want to change it until I have a well researched plan of how it ought to be.
Here's the list of my components:
qty1: CD player - Pioneer DEH-1500
qty 2: 6 1/2" speaker - Pioneer TS-163P (in cuddy, not currently hooked up)
qty 2: 6 1/2" speaker - Pioneer TS-1680R (by side of rear bench seat)
qty 2: 6x9" speaker - Eclipse 8392 (by side driver and passenger feet)
qty 2: 10" sub - Kicker XPL (under bench seat)
qty 2: 500W amplifier - Kenwood KAC-7495 (under bench seat)
I have two batteries on individual switches so I can listen all day and still start for the run home. Here is an album with some pics: http://pg.photos.yahoo.com/ph/wagnerboats/my_photos
A quick search online netted the owner & installation manual for the CD player and the installation manual for the subs. The sub manual details exactly how to build their enclosure (currently they are free air...). The structure for the rear seat will be rebuild to provide 2 1.0ft^3 sealed enclosures for the subs. I could not find manuals on the amps or other speakers.
My goal is to make the most of the components in hand by rewiring and building enclosures. We do a lot of floating and beach time so the stereo definitely works hard when we are out. I've played around with audio in the past, done alot of instrumentation set up during my career as a Lab Engineer, but am not a boat audio expert like the peeps here.
Any advice, input, tips etc. on how to set up the rest would be greatly appreciated!

[riverbound]

I am assuming the amps are 4 channel amps.
Wire one of the amps to power all the 6.5s on seperate channels.
Wire the other amp to power the 6x9s to 2 channels and bridge the other 2 channels for the subs. Then build baxes for the woofers. The woofers definitely need to be in sealed boxes.
This will give you the best sound without having to replace any of the equipment you currently have.

[ECeptor]

The amps are 4/3/2 channel.
Subs and 6x9's on the same amp...my initial thought was subs alone on one amp.

[Havasu Hangin']

The amps are 4/3/2 channel.
Subs and 6x9's on the same amp...my initial thought was subs alone on one amp.
I would put the subs on their own amp (I'd buy a class d). Every system I've heard with components and subs on the same amp, the components distort when the subs are hitting hard.
It's too hard to get them balanced, and enough power with one power supply.
On the sub install, it might be easier to build some boxes, and just bolt them to the back of the pedestal, rather than build a new one. The subs will just be recessed 3/4" or so...but you could use the same grills.
Just a thought.

[ROZ]

Since you want to use the current gear and don't want to run one amp in a 3ch mode, consider hooking up the cuddy to the headunit, the 6x9 and remaining 6.5 on one 4ch amp, then bridge the 4ch to a 2ch and hook the subs up to it...