More pix added.
Once you remove the plastic trim that the seatbelt passes through .... I'm trying to remember here... and possibly the window trim, there is a 4" thick piece of foam on each side that the cables can be passed under or beside. The foam blocks are under the outside edges of the wall behind the seats.
I replaced the rear speaks with Focal "sub" drivers using a custom adapter. The P/N is something like 5L. They're small but produce decent bass. I didn't want to eat up the already-small trunk with a sub box. The rear speaker cavity opens up into the gas tank area so I stuffed some foam in there to seal it up a bit.
I put foam in the bottom of the rear fender wells to support the amps and then anchored each one with a metal strap. You can barely see the anchor in the Alpine photo in my album (behind a cable on the left).
The great thing about putting the amps there is that the air coming into the cabin exits through vents in the fender wells. So if you you have the fan running, you'll have air flowing past the amps.
One thing I noticed when replacing the door speakers is that they were wet after it had rained. So when I installed my new Focals, I built a little shield over each one to keep the rain off.