As EMDDIESEL stated, I have the Center cushion sub from JBL. It is a wonderful addition to our RAMS. I debated the rear seat model but I needed the room to put stuff in the back on the floor (Not on the subs) As long as you use a high wattage amp, You'll get great sound out of the center seat sub.
The comfort level of the center seat leaves alot to be desired. It is a solid plastic casing with no cushion. This did not bother me because no one ever sits in the center. If this is a concern for you, get the 2 rear sub enclosure.
I am running an Alpine V12 2 channel 450 watt Amp to push the center sub. I'm also using the same model to push a pair of Boston Acoustics 6. 5 pro separates for the front. These separates come with crossovers and work very well. I also use a 150 watt amp to push a pair of BA Rally 6 1/2's for the rear. All the Amplifiers are located under the seats for a stealth look.
I use a Preamp Alpine model Head unit with 3 - 4 Volt RCA outs (Front, Rear, Sub) It is better for sound to run out of a preamped RCA. If you take an Amped unit, add a line level adapter (which brings the amplified signal to a non amplified level ) Then Hook it up to an amplifier yor are going to get some distortion of the music. It may not be as noticeable in a sub but it will be in a front or rear speaker setup.
IMHO, If you want to build a system, Add the Sub woofer with a new head unit and leave your stock speakers alone. (for now

) Most new head units come with a Subwoofer preout which makes it easy to wire in your new sub. It also gives you the feature of being able to adjust the Subwoofer depending on the type of music you are listening to. When purchasing the head unit remember to allow for expansion. Pick one with RCA preouts to run new amps when you add them.
Good Luck