Right, it was all assuming you had a bass box (sub woofer)
If you don;t then 6x9's should be ok, if you have a sub woofer, then DON'T BOTHER
Ok assuming you had a sub woofer, the vibrations from the air would push the cones up on the 6x9's (if on parcel shelf) which would cause damage to the cone! The sub and 6x9 would try and play certain bass notes, but would cancel each other out too!

Ok first step is to UPGRADE YOUR fronts or amp them (if they are good enough) The music comes from the front, this is where the sound stage is! Like a concert, everything comes from the front, if everything came from behind then it would sound 'weird'! Imagine if you were talking to some one, the other guy was behind you and you wasn't looking at him! It takes more concentration in understanding and comprehending what is said! So fronts are the most vital part!
In order to get the most out of the front, AMP THEM! The Headunit will give 20-22(headunit turned up before distortion, so 75%) watt rms each max (this is from a good headunit too) imagine if you got the full potential without distortion, so say 40 watt rms, that would make a HUGE DIFFERENCE instantly! Am I not correct?