hey here are a few pictures of some clean set ups and maybe you can get some ideas
O and i would reccomend staying with a good ported box and not closing it off from the back seats with a full wall b/c it won't be as loud then and u will def notice a nice increase in sound in not having a pre-fab box

anyway pics..






hope those help you out a little

 

Don't put an amp upside down. They fry after a while due to decreased ventilation. Caps ftl. An extra battery or 1 Optima is the way to go. There's nothing you can't do to a system. Just get creative and make it clean. Your box is as big as mine in my B5, but I got 1 Kicker L5. I got it hooked to an Autotek 1200.1 so I'm peaking at 1324 watts and RMS is about 600-700w. I love it cuz its clean and accurate bass, unlike RF and JL. That one is about 144db and no cap or extra batteries. I had a M Mojo 1800w in my A6 hooked into a Hifonics amp. It was peaking damn near 2,000watts and pushed 152db's with the seats down. It was downright retarted for a single sub with no extra batteries and a stock head unit. But that's all in the past. Now I take out my Kicker to track my car and put the box back in when I cruise late at night. I don't bump loud anymore. I got it as low as possible, just enough bass waves to let me know its there. I'm selling the Mojo as well and I'm trying to find a way to install 2 Kicker 8" shallow subs for my B6. Somewhere in the trunk, rears seats or rear deck. I don't even want them to be noticed but a nice clean bump when I ride. I'm a lot more subtle now than 2 years ago when I started driving. Trust me you grow out of the "letting everyone know what I'm listening to" phase. But its a nice git up and you should put plexiglass and LED's to light up the system and make a nice trunk.

 

to add what euro said about the amp over heating you can get fans that blow onto the amps.. they have some nice computer type fans that will work nicely for what you will need

 

My amp already has a fan that blows air out of the AMP and its regulated digitally i believe.
On the LCD display i can control various things including fan speeds. My amp never really runs hot because i have it mounted on the top of the box of my subs and its positioned right under the rear deck where air always gets there because i drive with open windows all the time. But i know what you guys talking about im going to build a custom box for it and hide it under plexyglass and have a 2 120mm fans cooling it. im making a photoshop of it if it works ill show you what im talking about

 

 

I've seen Kenwoods fry as well. But if you got proper air flow they will last pretty long. I mounted mine in the backseat

 

yeah i dont know how people mount their on the back seats because i would think there is a limited air flow there since the box is right behind the amp or if you look from outside of the car amp behind the box.
i think im going to make carpeted box with 2 120mm fans from computer or something and have it blowing out of the box and have two plowing in the box. plus plexiglass and blue colored fans would m ake a pretty light show lol

 

I have a clarion 4 channel that drives my speakers and when I used to have a big box the only place to mount it was under the rear deck upside down then when I took the box out I still needed to put tools and stuff in ther so I left it been maybe 6 years now no problems so far...

But yah its only driving the speakers at 60 watts each RMS not 1200 er so for a sub.

I got a 12 kenwood sub and an sony explode 2 chanel amp bridged with the amp mouted on the side...this is my truck box which I switch back and for from audi to truck in winter/summer ...
With the amp mounted on the side pushing close to 600watts it smells like burning electronics and gets too hot to touch

 

there isn't anything wrong with mounting an amp upside down.. that is def not an issue so don't worry about that

 

Well here's an idea. Since I never wanted to risk burning a $500 amp I made a drawer-type shelf braced to the top lid of my friends 530. I drilled a buncha holes on the plexiglass holding the amp to provide proper ventilation and put neon bars (2 years ago so LED's weren't so hot) around it to create a cool blue glow. And it would slide out when unlocked to show off the amp. It was cool, out of the way and right side up