A nice and more compact sub/amp combo is the Kenwood KSC-SW1. It's very small, includes wires, installs to any head unit and sounds great for it's size. It will fit right under the seat and take up no foot room whatsoever. It add no mids just low end but it means you can turn the head unit bass down and the let the sub do the low end work. It rounded out the sound for my lackluster saab stereo perfectly and I will install it in the Sonata in the near future. Pick one up on ebay for around $150 and I guarantee it will beat out the upgraded Sonata sub.
Kenwood KSC-SW1Just read the reviews. It's an impressive little unit. It includes all wiring also. Best Buy (if you trust them to do the work) will install it for $50. So for $200 total you can get a nice sound upgrade for the low end. I'm not one of those thumping rap music types but when I listen to Jazz for instance I love a nice clean and deep bass and this little sub really did the trick.