Beaner is right, if you really want to keep the stock headunit, you can. However, in all honesty, I would buy a new headunit hands down. Our stock headunits can often times have problems and devices like Beaner suggested are fairly expensive (maybe more than a new headunit).

If you search a good bit on the internet, I bet you can find a good, matching, $100-150 headunit that is ipod, subwoofer, aux, mp3 ready... You'll have to also get a headunit harness, but theyre about 10 bucks or so... Also, I bet you will get better sound quality through all of your speakers by simply getting a new headunit. I did for sure...