If you wanted something real clean looking you could do something like this:
http://performance.clubrsx.com/fiberglasssubbox.html just sans the sub. Then mount it a little further back in the trunk. Just to get ideas going in your mind. You could also try going to an auto stereo install place and asking for an estimate to put the amp in that spot. If it's a bad spot they'll probably tell you that they won't do it and give you the reason or suggest better spots (they don't have to know you plan on doing it yourself).