Most of your questions have been answered in messages here - I'd refer you to the messages but maybe if you try the search they might pop up.
You are correct about the rear speakers - both signal and power leads to them. There's a really good thread on that which is, I believe, this message:
https://www.crossfireforum.org/forum...ead.php?t=9308
As for the factory amp and speakers, you have many options.
I wired my aftermarket head unit into the car using a harness connector that goes onto the aftermarket head unit.
Then for my mid and high-range rear speakers I used the aftermarket head-unit speaker-level outputs. For my sub, I used the aftermarket head-unit sub-output.
The sub has an integrated amp so I also connected the remote power on lead from the aftermarket head unit.
I left the factory amp to power the front and rear factory speakers. They all run out of the "front" channel of the aftermarket (and factory) head unit so I can do front and rear balance.
The side door speakers benefit from installing a crossover which is also covered here though many aftermarket head units have high-pass filters settings that can be used to accomplish much the same thing if you isolate those speakers in your wiring plan.

Details Here