I'm in a similar situation myself and thought I'd share....

I recently replaced my older alpine HU (m-bus, rear ch. pre-out only) with a newer alpine unit
with all three sets of pre-outs, sub control, bass/treble center frequency settings, etc.
BIG DIFFERENCE.
The ability to tune the bass and treble frequencies to suit your speakers makes a noticeable difference in clarity.
And being able to fade to the front speakers without cutting and distorting your signal to the sub is the way it should be.
With the ai-net adapter... my ipod has never sounded so good. I've got a 4ch amp too (eclipse ea3422)
but need to find some decent 6.5" components and 6x9's to push with it to complete the system.

The rears I'm not too worried about, but which 6.5's can play loud and clear from down by my feet?

-T