Ok guys, here's the setup i'm planning:

Head Unit:
Keep the stock unit. I've had two head units stolen out of my civic in the last month and a half. I don't really want to have to worry about that with my new A4.

Front Speakers:
JL Audio VR525CS 5.25" Components

Rear Speakers:
JL Audio VR650CX 6.5" Coaxs

Sub:
JL Audio 10W0 10" Sub. I don't need earth shattering bass so I figured a 10 would do nicely.

Amp:
Sony XM-405EQX 5 channel amp 40x4 + 100x1.

What do you guys think?

Got the speakers and sub for $500 at a local audio shop. Ordered the amp online for $300. $50 for a sub box and then $150 for installation. It was a little more than I had planned on spending but I think it will be worth it.

Do not get a Sony amp. They are overpriced and have decent sound quality at best. I would spend a little more on the amp and front speakers and skip the rears altogether. Depending on whether you have the Bose system the install will either be difficult or really, really difficult with the stock head unit. If I were you I'd replace with a detachable face unit. Just don't forget to take the face and it won't get stolen.

I really want to keep the rear speakers, I much prefer the sound with the rears. What amps would you reccomend for a 5 channel setup like mine? I could get a 4 channel amp to drive the speakers and a mono amp for the sub but I was hoping to keep the amp costs below $500. I was also looking at the MTX 405 Thunder (also 5 channel) which is about $110 more.

I would agree with the amp. Go with something like Phoenix Gold, PPI, Zapco. It will cost more but will be worth it.

and I really think you should reconsider not getting rear speakers. Think about it this way, when you listen to music at home, do you have speakers behind you? No, I didn't think so. So why would you want to distort the soundstage in you car by having half the sound coming from behind you? It doesn't make sense to me, and I think it's a huge waste of money.

As for the amp, five channels, decent sound quality, enough power, and flexible connection options (which you will need if you are sticking with the stock head unit) for under $500 is not possible. Plan on spending at least 7 or 8 bills. Your best bet is probably Soundstream for a configuration like that.

I don't mean to sound like I'm trying to take the wind out of your sails, but I just think that people need to get the idea that they need rear speakers out of their heads. Just spend more on a great set of 5.25" separates.

Bose builds some of the crappiest speakers available today, and they use massive equalization in the electronics to compensate. If you try to run an aftermarket speaker on a signal intended for a Bose speaker, it will sound aweful and could damage the speaker. If you have the Bose option, its all or nothing. Keep it all, or get rid of it all and start over.