If your setup is like mine the 6X9's in the rear deck are being used for your subs. The rest of the speakers in the car are your mid range and high range speakers. All mine are ran by an amplifier mounted on the rear deck.
I like lots of bass so I have decided to replace the whole system. You have to decide how much bass you want and how radical you want to get.
The least expensive would be to replace your speakers and keep your current radio and amp. I would suggest a basic 6X9 two way and just disconnect the tweeter. Brand is just a personal preference once you get to a certain level. (Alpine, Pioneer, Keenwood ect...) The smaller speakers need to be as efficient as possible because the amp isn't that powerfull OR you could just take my path...JERK IT ALL OUT. Big amps big speakers.