To be honest, I'm not really sure since I haven't taken that part of the car apart, here's some things to things about :
You *might* have room back there, but you most likely need to do some cutting of things to get airflow into that space. Also, consider that the fuel tank is partially situated under there AFAIK, so I would strongly reccomend you not drill anywhere in that area.
There are some other good options, I'm probably going to put the amps under the front seats, and I'm sure if you played with the cargo tray under the floor of the trunk you could fit something under there, and just add some holes to the cover and maybe a fan.
If you end up going under the rear seats, be sure to get some pics...I'd like to see how it turns out. Good luck!