The factory sub is a "Free Air" or Infinite baffle 8" sub. This DOES matter, not all subs are designed to work without a box, and the ones that are, are not designed to operate near the RMS or Peak power ratings listed. I don't know whats size is in the doors but four total in the doors, on the rear deck lid it looks like two 3.5" with a 8" sub in the middle, and I believe they through tow tweeters up in the A-Pillars, for a total of 9 speakers. If I had to guess, it's 6.5" in the doors. I'll modifiy this post later with Infinite baffle sub alternatives and amps to match them.
Here is a link to crutchfield's selection of 8" "Free Air" subs
http://www.crutchfield.com/g_520/Component-Subwoofers.html?tp=111&nvpair=FFSize|[rank6]8%22&nvpair=AG_General_Features|FFFree_Air
I like crutchfied because they have the manual listed for each one, and you can read exactly how it is supposed to be hooked up with power recommendations and what not.
I'll go ahead and throw out that I work at Best Buy in the Mobile Installation Bay, this is my personal opinion and what I've been looking at installing in my dart when I get one.
One setup I would recommend is the 10C88 Kicker Comp Sub, Kicker 11DX250.1 AMP, and Kicker ZCK84 wire kit. (you can use the PK8, however I hate the fuse holder it comes with and would swap it out with a better one). Reasoning at end.
For the Install you'd just tap-in to the rear speakers and run the wires to the amp with the power and ground kit, instal the amp and sub, set the amp to high inputs and signal sensing, tune the gain, and she's ready for some noise.
You can use any 8" sub that supports an infinite baffle setup, just make sure you don't push her too hard our you'll be lucky to make it through a song without blowing the sub.
The reasoning behind it:
Let me start with the amp. This amp has a lot of really cool features that make this install easier. The Amp supports signal sensing and high level inputs. This means that if you tap into the rear speaker connections, you can run those wires straight to the amp, and the amp will be able to turn on, and amplify that sound to the sub. You do not need a line output converter, and a place to put the box that's around 1"x3"x2". This amp is also able to be mounted upside down and dissipate heat build up (not all amps can do this). Second is that it puts out around 140 watts of power @ 4 Ohms; we will circle back to this in a minute.
Now the sub, this is the part that requires some reading. It says that the speaker supports 50-100 watts RMS. If you read through the manual you can see that in does indeed support an infinite baffle setup, and a good starting point for power is going to be 55 since that's what the ported power is rated up to. The reason that I choose the 8 Ohm sub is because 8 is greater that 4. If at 2 Ohms the amplifier is putting out 250 watts of power, and at 4 ohms its putting out 140 watts of power, at around 8 ohms it's going to be putting right around 70-80 watts of power (and the amp is not struggling to produce this). The more resistance the lighter the load on the amp.
Now because this is all being installed in the deck lid, you really gotta watch that infinite baffle setup. In a normal sealed sub box the speaker creates a vacuum in the box; when the speaker pushes out, the vacuum pulls the cone back in. When you don't have that vacuum and you put the same amount of power to the sub it can't retract and you can easily blow the sub below its RMS power.
If your piecing together a system and want to make sure it works I would ask and installer before you purchase your items, it can save you tons of money.