I have the Sony system and first replaced the sub with a Kicker 12 and then upgraded the door speakers to Infinity Reference 6852 or maybe 32 speakers. I can't remember the exact model but it was one of those
HUGE difference with the door speaker upgrade. I also left the factory tweeter's plugged in on the A-pillars to fill in the sound a little better there too. With the door speakers being so low down in the door, I felt I needed to keep some of it up near eye/ear level.
So the factory Sony amp still controls all the door speakers and the tweeters and the sound improvement was quite noticeable. Once you handle and take out the door speakers and compare to a new quality set, you can quickly see why