Ok, go to the bathroom, grab a cup of coffee and find a comfy chair to sit in because this is possibly my longest post ever
First off let me say I am by no means a "professional" audio guy but do some tinkering so here's a few thoughts of mine. First off, don't waste your time putting any speakers under the seats for your front stage. The front speakers are better off in the doors or in a kick panel type setup like these
http://cgi.ebay.com/Q-LOGIC-Q-FORM-...5|66:2|65:12|39:1|240:1308|301:1|293:1|294:50
You don't necessarily need a component speaker with a seperate woofer/tweeter, just a good 2 way speaker mounted in the door would also work fine. A component system like what is used in the kick panel setup are going to require more power so an amp would be needed. A standard speaker with a lower power requirement would probably do ok running off deck power but would most likely benefit from an amp also.
Subwoofer placement is kind of a tough one because every speaker, enclosure & vehicle is going to sound different. If you put them behind the front seats facing each other you may run into problems with the sound waves crashing into each other and sounding bad. I suppose if you mounted them angled slightly facing the front that might work. You could go with the standard dual sealed box route, somthing similar to this
http://cgi.ebay.com/New-10-Inch-Dua...5|66:2|65:12|39:1|240:1318|301:1|293:1|294:50
Typically this would go in the very rear of the truck and speakers would face the tailgate allowing the sound to bounce of the rear gate/window area.
Couple other ideas would be to make a smaller enclosure that would go in the center console area with a downfiring sub, bass would be right up front and therefore would not need to be as loud or require a ton of power.
I've also thought about builiding a thinner flat box for the rear that would go across the entire rear floor area behind the back seat using a new slim design sub, again in a downfire type design. This way you could still load stuff in the rear and if the box was carpeted it wouldn't look like anything special.
You could get a multi channel amp to run both the speakers & subs if you want to simplify things. Most important thing is to match the power requirements of the speakers & amp. No point in having 1,000 watt subs and 50watt amp. The other way is ok, more amp than what speakers need. This is called headroom, where the amp is capable of producing more power than what you really need, just turn it down to a level before the speakers start distorting.
The alternator probably should get upgraded anyway from what you're describing. Here's some good charts to look at that will give you an idea about amps, power requirements and cable sizing. Actually the website in general is loaded with good info,
http://www.the12volt.com/info/recwirsz.asp
Here's a couple decent car audio places to get some deals,
http://www.woofersetc.com/
http://www.sonicelectronix.com/
http://www.crutchfield.com/S-kANsbFpmAAN/ (more expensive but killer customer service)
Oh yeah, don't forget all the sound originates from your head unit so it can only be as good as what that is capable of.
Clear as mud yet ?
