Better...not just Louder

I was looking to do some minor mods to the sound system in the hopes of makin it sound better, not just louder. I wanted to add an amp and a sub, but I was told that adding an amp with the existing speaker would be useless. I don't want to change the head unit since i have a 6 CD in dash, and don't see the point of changing that, unless I can get the same system but reading MP3's...(which I've yet to see...) So what do I do? I want sound quality...not loud distorted sound...do I need to change the speakers? There isn't much room for upgrade on the rears since the trunk bar runs about an inch away from the magnet below the speakers...