I disagree with running the rear speakers off the head unit, one of the biggest advantages to amplifying the stock speakers is that you will have a crossover built into the amp that can filter out low frequencies. Removing the bass from the signal going to the stock speakers will allow you to play them much louder without distortion. If you only amplify the front speakers you will get nice clean sound from them, but it will be muddied up by the distorted sound coming from the rear speakers.
Ideally the best possible option is to replace all the stock speakers with high quality aftermarket ones, and power them with a nice 4ch amp. then run a seperate mono amp on a sub. But if you don't have the budget for that and want the best sound for your money, going the route I described in my first post will get you good results for little money.