I was just wondering what can you add to a protege ES sound system without taking out the factory headunit?

 

I was also wondering if swapping a pair of speakers would make a noticable difference? And if I did swap a pair of speakers which ones should I swap?

 

Swap all the speakers for some good coaxials (2 or 3 way) first. You'd be surprised how much of a difference it makes.

If you were only going to swap out a pair, I would do the fronts

As for your first question, you can add anything you want using a factory headunit, so long as any amplifiers you add have high-level inputs. My brother had a bonneville with the factory headunit, he used 2 amplifiers, infinity speakers and a Kicker Solobaric subwoofer, and it sounded really nice.