Need to find a better place for a 1000 wat...

wait a minute, so do you have the subwoofers installed already?
If so, I would say just lay somewhere around in the trunk lol.
I have a 1998 Hyndai Elantra and that is my set up.

You could always mount your amp to the sub enclosure itself... That way if you need your trunk space, you can pull everything out at once. I have mine just sitting on the floor in my trunk and haven't had any problems with it. Another idea is mounting it to the back of your rear seat, inside the trunk. Just make sure that you don't have any pinched wires or wires being pulled on.