I plan on amping all six speakers to my 4 channel amp. The rear 6x9's have 4" speakers next to them, so is there a way to connect those two to one channel? My speakers will have enough bass to where I wouldn't need a sub.
Not at all. You would never finish installing a headunit then tear it back out to run rca's to it. Do it all at the same time if your planning on running an amp.
Hmm, I honestly wouldn't bother amping the 4" speakers because there is gonna be quite a power handling difference between the 6x9's and the 4" ones. Switch out all the speakers, power your 5.25's and your 6x9's, and leave the 4" ones on stock wiring, unless they don't work on stock wiring. I guess you could power both on one channel, but I'm not sure what the overall impedance would be on your amp, so getting the right amount of power to your 6x9's will be tough. (You can try it though).