To your second set of questions...
1)Your aftermarket HU can probably put out better sound than the factory amp, which is why you want to bypass it; if you don't bypass it, you ultimately get the amp feed in your speakers.
2)I don't know about the other stuff, but you could get an HU with only one set of RCAs and split that up using y-cables as many times as you want. Channels/2 = set of RCAs. Again, you can use Y-cables to get as many sets as you need.
