If you are on a budget, and want good sound as cheap as possible, I would say the first thing you should look at is your head unit. If you really don't need anything crazy, many of today's high-powered head units offer up to 45 W x 4 channels with RCA's for sub output.
Stage 1 ($200-$300): A GOOD high-powered head unit with stock speakers will sound pretty good. Look for a head unit with built-in "MOSFET" circuitry.
Stage 2 ($150-$400): Add a small, powered subwoofer box. You could probably build a really nice one yourself for a couple hundred bucks, and if you build the amp and sub into one box it's easy to plug in or remove (just run RCA's and power to the rear cargo area and install some jacks or quick connects). For a few more bucks you could buy a pre-built powered sub.
Stage 3: ($150-$350): Upgrade all four stock speakers.
Oh, as far as putting the amps behind the panels, I'd say that this MIGHT be possible, but the amps would have to be really small or you'd have to lose the jack and/or the compartment on the right side. There IS a lot of space behind them, but the shape isn't suitable for most amps. I would agree that you should consider one 5-channel amp if you think you'll eventually want a front x2/rear x2/sub setup, but they don't have to cost $800, and you don't really need 5 channels unless you often have passengers in the back. You could get by with a 3 channel amp running left/right/sub - you won't notice much difference from the front seat.
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