I am getting ready to do the same thing and here is what Im going to do.
First, the power wire from the factory harness is not big enough. You will need at least an 8 gauge, up tp 400 watts above that you will need a 4 gauge, wire that has a fuse block with 18" of the battery. Then you will need to run an 8 gauge for the ground no longer than 24"
Second you will need to find a ignition input spot, it can either come strait from the fuse panel of the head unit.
Third you will need to buy a line output converter that will change the factory speaker wire signal into a usable rca output. I own a Tsunami line output converter and it cost less than $20.00.
I have tried to ask several time if someone makes a wiring harness that will just hook up to the factory one but no one know if they do. I am curious if the factory wiring harness has an ignition that would work the factory amp. If so it would make running that ignition wire a lot easier. Also would keep me from having to splice into anything.