You can use the factory deck with any kind of speaker line level converter to change the signal from the facory speaker to RCA. Don't skimp here, the cheaper you buy the worse the sound Q will be.
If I can make one suggestion if you like the current sound, but just want more bass do a simple eclosure in the trunk remove the factory sub (to all bass into the cabin) then get a small amp like JL 250.1 or equivalent.
If you want to go higher end, and get this car to sound good and really rock you will have to lose the deck and line level crap - but remember, this will cost you $2500-4500 easily if you use good equipment.
Here is a set up I used, and the sound is really, really good (not to toot my own horn, I just think my guys did a nice job on this).
1. Kenwood DVD 6017 deck with trim part installed $1380
2. JL Audio 450.4 (150x2 and 75x2) and 500.1 (500x1) amps $900
3. JL Audio 3 way 653XR series set (6.5", 4", tweet) in front $330 (ebay)
4. JL VR series 6.5" for rear fill installed myself $120
5. JL 8W7 sub in rear deck with box $550
6. Wiring and fuses and labor (re-run all speaker wire) $400
7. JL Bass knob with self install $40
8. Rear camera to play on the deck $200
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TOTAL $3920
If you use your factory deck and line level, you won't have the $1380 on there, or the $400 for wiring and whatnot, but you will have to buy other equipment to make the line level conversion and have to pay to have that installed...
Whatever you do don't change anything unless you are a music lover, you are not happy with the factory sound, and you are sure you want to dump the cash into the project. I found once you do one thing it leads to another and another...