I've upgraded mine, and I have a vert. I also didn't want to lose trunk space. I took out the factory sub, and mounted a better quality one in it's place. The screw holes did not line up, so I drilled new holes in the plate. Next, I used a bunch of dynamat and basically made a sealed box by putting the dynamat all over the framing members between the trunk and back seat. It took a while, but we got 98% of the air leaks sealed off. It sounds nice, and I didn't lose any trunk space, and no one knows that I have something aftermarket in there.
for the amps, I mounted them in the space for the spare tire (no tire is in there on the zl1's) and I just removed that foam thing that holds the air pump. My air pump just sits in the trunk now beside the vert cover.