Back to the original issue at hand.
There is NO need to swap out the stock head unit in order to put in an amp and subs. I have an entire aftermarket system in my X and still run the stock head unit. Best Buy and many other places sell a small unit called an RCA converter wherein speaker wires go in one side and through magic the signal is converted into RCA out the other side. Some even have gains built in...
This will allow you to run the RCA signal to the amplifier of your choosing. For sub frequencies, i would NEVER go with anything smaller than a 10" sub due to the fact that anything smaller has problems producing the lower tones and hard hitting thumps. Depending on the genre you enjoy - sometimes even a 10" will strain to produce audible tones.
If you decide to go with a 10" or 2, be sure to spend the money on a good set - JL, Kicker, the new P3 Rockfords, or even the higher end MTXs. Dual voice coil is NOT a requirement and don;t let anyone fool you into thinking the duals are louder - the DVC subs are simply used in order to bridge amplifiers down to lower resistance levels in order to take full advantage of the amps ratings at lower impedances.
On the subject of amplifiers, this is another area you do NOT waste your money on cheap equipment. i am a huge fan of Crossfire amps b/c they are mid-level and operate conservatively on the given power produced to them from the vehicle. However, JL amps are great peice of equipment and i would suggest buying a 5channel amp now and at a later date you can upgrade your doors and apply them to channels 1-4. Additionally, the JL amps have a good built in crossover for the 5th channel.
just my 2 cents