My system for the longest time had a 10" 1800w Pioneer Competition Sub in a Ported Truck Box on the floor board. Hard for people to get in lol. But I didn't care, it hit hard.
However I am building a new system. First off, the Door speakers aren't hard to add if your car don't have them, I've honestly never heard of such a thing. I dislike my Dash Speakers even tho they are aftermarket. I have some MBQuartz in the doors and they sound amazing. The Dash Speakers overwhelm them and I can hear sounds I don't want to hear.
Anyway. I'm building an enclosure to replace the drop top, since my car is strictly hard top now. It will house 2 JL Audio 600wRMS 13" Subs. Before I decided to go all out, I was developing an enclosure for just one JL Audio 13". Under the Top when its down, is enough room for a very decent sized Fiberglass Enclosure. However if your not ok with fabbing up such a thing, JL Audio makes a dual 8" Ported Enclosure which sounds and hits really hard. And its virtually the same size, if not a lil smaller than the stock BOSE Sub. It fits in this location quite well, top down, up. And loooks pretty good too.
The Bose Sub is worthless. The Kicker and Infinity Hideaway subs are worthless. I've been working car audio for a long time and yes, while you can get some decent sound from those hideaway subs, they just aren't all that.
I've put one of these twin 8" JL Audio enclosures in my car just for test purposes and from everything I've seen on here for people's bass, I would have to say this would surpass them with ease in audio quality and bass output.
http://www.amazon.com/JL-Audio-CP208LG-W3v3-Subwoofer-Subwoofers/dp/B0082DIYBO
If you want to keep it simple and small, The Self Contained units are good for this.
My system is a lil out there for any of the typical Purists. I have an 8.4" Octa Core Computer in the Dashboard connected to a 5V Preamp Output Sony Reciever (top of the line in sony's book and only radio that has a legit App Remote program for Android or AOS) Then from there I have a 4Ch Amp Bridged to 2 Channels for the Door Speakers and a 1500x1 RMS Mono Amp connected to the 2 13's. But the enclosure isn't built yet since I'm lazy and overworked at the same time.