You always need to be careful when drilling into anything in a car, especially the trunk. Crawl underneath and see where the fuel tank is, various lines, hoses, etc. I try to avoid drilling into the bottom of the trunk, because it invites water, fumes, etc, into the inside of the car. If you want to put it in the trunk, I'd cut a sheet of plywood to size and mount the carpc to it, then place it in the trunk.
You should find a few forums for your particular car and see how people have mounted amplifiers and subs.