I had my Sony amp right next to the spare tire and it didn't seem to mind the heat. However now I'm paranoid about getting things stolen (I've had my car broken into twice already this year, and once last year!) so I'm thinking that I will be installing my amp behind the side panels that are above the rear-seat arm rest - basically right below the rear quarter window. This would fit best on the passenger side as there are some relays on the driver side taking up space. However, there's plenty of room there, and even if your lower quarters are rusted through not much water willl splash that high up - so it should be safe. There's also tons of air in that compartment so heat shouldn't be a problem. Plus, it's totally hidden and would take a thief a lot of time and effort just to find that amp as you'd need to remove a lot of panelling to get to it. The only shitty thing is if you want to reconnect things or tweak the crossovers you'll need to remove all those panels, but I don't see that as a major issue.
As for the rear storage compartment, well, I usually keep a blanket and some towels or a chamois. Another good place to hide things is in that little compartment even some Supra owners don't know exists - the rear window washer fluid resevoir compartment. It's just big enough to store a face plate or a house key or something valuable.
- Mike