Help me plan my setup

Well, I wont get into the typical "x" brand is better than "y"... so on the basic idea of your system, sounds good.

The rear fill (the 6x9s) are just for some extra sound, they can be totally removed and the system will still sound great (from the front seat). So imho, there is no need for the extra cost of putting components back in the rear deck. The 6x9s should be fine.
Your back seat passengers will be glad they are there however, as oposed to hearing pure bass.

As for amps, you have three ways to go (as i see it);

1 - you can run one 4 chnl for the speakers, and a seperate 1 chnl (2chnl bridged) for the sub. This would give great sound, as much power as you can afford, but at the cost of more space, and more wiring.
or
2 - you can run a 4 chnl amp with the 4 main speakers run in parallel off of 2 chnls and the sub run off the other 2 chnls bridged together. This gives good sound BUT you loose either your balance or your fade, but you only need space and wiring for one amp.
* Note: this would be a good set-up if you only run the components in the doors and the subs, with no rear fill.
3 - you can get a 5 chnl amp and run all 4 speakers plus the sub off one amp. This gives full sound, with only taking up space and wiring on one amp, BUT 5 chnl amps aint' cheap!!!
*Note: since you like Alpine, they make a series called the v12 (unless they changed the name again) that is a 5 chnl with like 40x4 and 100x1 or 50x4 and 150x1 .... something like that.

Oh, just a side note, whatever you decide to do, run good quality speaker wire, and rca cables down one side of the car, and run good gauge power and ground wires down the OTHER side of the car, never lay them side by side. It begs to cause interference by EMF / induction.

Hope this helps,
Dave-

OH... BTW, e-bay is your friend... I just got some tunes for my truck: got 2 sets of infinity's for $74 a pair, including shipping (120 local store price) and a 4chnl 80w rms Phoenix Gold amp for 130 inc ship (210 local store price) and no tax.

I'll agree with the above poster ('cept for the wire quality statement, but to each his own). Also, I'll add some advice. Without extensive processing, you'll get your best sound from those tweeters by aiming them at the OPPOSIT passenger. Meaning, aim the passenger tweeter at the driver, and vice-versa. This will equalize pathlengths, and it will sound more natural- instaed of pulling the sound so it sounds like it is right beside you.

Most of the 5 channel amps have a subwoofer level control. Also, a lot of your better head units have a subwoofer level control on the outputs.