You could put a bass knob control up front as that might help when you do have rear seat passengers who don't want to sit right in front of two subs.
As for where to install - that depends on the amp. and how much you want to spend for installation. If the amp is small enough, then you may be able to hide it near the cd changer bracket. I had mine mounted onthe back seat which worked out well when I needed/wanted to make adjustments to the amp.
Under the mat is not a good idea (assuming you plan to cover up the amp w/ the mat on top??), because the amp will get hot and needs sufficient air for cooling. You could just mount the amp on top of the trunk mat flush against the back near the rear seats. That would work. Make sure your installer does a good job of tidying up the power connections if he does this, as its possible you get water or snow in the trunk.
Hope this helps