1. I had my amp in my old integra mounted under the passenger seat...I still like that idea.
2. Run the wires in the same place the factory harness wires go through. There should be a rubber tubing with these wires for the oem speakers, locks, windows, etc. Just use that.
3/4. I'm confused with what your goal is. Your Polk 6.5's are coax's, that have a tweeter in the middle. Are you also going to be keeping your OEM tweeters on the top of the door panel? (I assume your Accord has them there). If this is the goal, leave the 6.5's running off the amp, but have the OEM wire still going to the tweeters at the top of the door. Don't do what Marshy did and link the OEM speaker wires to the ones coming from your amp.