I'm running a 10" MTX sub with a kenwood 500W amp in my car. It sits in a single box tucked in the opening in the trunk on the right hand side. It adds a nice deep rumble to the car but nothing too extreme. First what type of music will you be listening to? 10" subs are good for tight bass great for rock, 12" subs are more for hip hop and rap or even techno. But either one could be used for either purpose. JL, Kicker, Pioneer, Alpine all make great subs. So once you know your size, pick your brand, then find an amp to go along with it.
There are a lot of options you could go with MTX thunder form is one example : http://www.crutchfield.com/p_236MUSB....html?tp=61653
. These boxes are custom made for the car and fit great and look stock. JL makes one with a sub and an amp all built in one if you do not want to do separates. If you're really in doubt go to crutchfield.com and take a look. Then do a search for sub install on the forums to help you run the wires and get it all powered up. Hope this helps.