Replacing speakers with aftermarket one's will always make a difference, but you have to be really careful with the output you get from the standard head unit...
From what I have read here, there are 4 cables per 6x9 as standard (2 off +ve and -ve's), because they are effectively 2 different speakers per 6x9. They are at different ohm ratings (one pair at 4 ohm, one at 8 ohm, I think), so the amp is at risk of over heating if you use the wrong connections to your new speaker.
Do a search using the Search function, it should be able to explain more.
As for the standard head unit and connecting to another Amo, I think there is a pre-out ont eh head unit to do so, but as I never even considered doing this (my standard head unit was screwed) I have not researched it.
Again, run a search and it should pop up with something.