ditch the 6x9s completely, amp your front components ( you dont even need rear fill...
get a 12" sub in a sealed box, dont bother with a ported box if you listen to a variety of styles, as porting limits the subs performance to certain styles and you can easily stick it to one side of the boot, leaving you room for the shopping
if your not into heavy heavy bass, then a 10" would suffice, but youd sacrifice some of the deeper bass... have a look on ebay for stuff...
one point i cant stress enough is, make sure the amp is up to it, no point buyin a 1000000000w RMS sub if your amp is only 100w RMS as youll end up cranking the amp up full, causin distortion and burning the ass right out of the sub ( the voice coil )
if you can afford it, get a monoblock amp for the sub, and a seperate 2 channel amp for the front components, or a 4 channel which can be bridged to 2.. no need for extreme amounts of RMS in the front speakers, as youll have no back fill to compete with ( e.g. 6x9s ) theyll sound lovely and clear, and the setup will be the doggies... go for something like 70 - 100w RMS for the front speakers..
this is, after all assuming your not planning a showstopping ICE install ??