I have put my amps under the seats in every vehicle I've ever owned - 3 sports cars, 2 trucks and now my XJ. There's just enough ventilation under there to keep things operating properly.
Like the others have said, it depends on your water exposure as to whether or not you want to go under the front seats. The way I see it, the rear seat doesn't really sit up that much higher so it might have a little advantage. But if you've got that much water in the cab, there are many other plugs & wiring harnesses that are going to have water exposure as well (so you're hosed anyway)! Plus the prospective thief might think to flip up the ol' rear seat. Poof! A nice shiny new amp, very easily accessible.
I have had a couple of vehicles broken into over the years, and the bloodsuckers were able to jack the head unit or speakers - but never the amp. A car thief is on a limited time schedule, and removing a seat just does not fit within that time frame!
The main thing to remember is to seal up all of the holes that you drill for mounting the amp, ground wire, etc. Just use RTV sealant on the inside and outside of the vehicle to make sure that no moisture can make it through the holes you drilled.
Most importantly of all - take your time. I know that you're ready for the tunes ASAP, but I have had to undo some installations in the past because I just wasn't happy with the way I had done it the first time (in a rush).