Thanks for your response. I tried them as my front speakers and while they sounded fine they were weak on the bass.
The 6.5 s in the back can't provide the bass and you can't really hear them anyway.
So I wired the 6x9 s in the front door as my rear speakers instead. My thinking was the original setup by infinity used the 6x9 s as the bass. Therefore wiring them as the rear speakers stay true to that.
Yeah you're overthinking this a bit.
That new radio puts out the same audio signal to all 4 channels. FL, FR, RL, and RR all get the same signal. Hooking the 6x9s to the rear channel will just throw the fading of the system all off. The 6x9s and 3.5s need to be on the front channel. And the 6.5s need to be on the rear channel.
Basically what you have done here is install speakers that have a higher power handling capability than what your new radio radio is putting out. Basically the components are stiffer to handle more power, but your radio that only puts out about 13 watts RMS per channel, doesn't have the power to move these stiff components. So your new speakers actually sound worse than the old ones. The infinity system was matched as far as power output from the amp, and power handling on the speaker side of it. That's why it had more bass. The speakers were matched to the amp.
A lot of people think that just throwing in expensive high end speakers with a high power handling rating will sound good hooked to just an aftermarket deck, but they won't. Unless you amp them to the RMS rating they have, they will sound like crap. In cases like this, cheaper, lower power speakers will actually sound better because the deck can move them with the small amount of power it is putting out.
So long story short, the only way to make the setup you have now sound better, is to get a 4 channel amp with an RMS rating per channel that is close to the RMS rating of the speakers you have.