I paid to have an audio shop do the install, but I told them the Premium system was unpowered so they would not need a line out converter, and to remove the factory amp. I have installed stereos before, but I paid to have this done because they built a custom sub box in the trunk so it would not take up a lot of room, and I wanted it to be done right. I was not familiar with the Honda's differential balanced outputs, so I didn't want to mess anything up. I also wanted the tweeters done right in the factory A-pillars, so I knew a shop would have experience doing the work. I did not have the time to tackle the job myself, even though I would have enjoyed doing it. I posted photos of the installation with a PDF of the wiring diagram for the Navi system with Premium, and the external amp. So that should help you. The PDF link is at the bottom of the post after the pics. The shop told me the wiring diagram was accurate and made their job easier to do.
http://9thcivic.com/forum/threads/2013-civic-premium-audio-system-navigation-stereo-upgrade.10207/
You can do all the wiring at the factory amp. I don't know where the amp is installed in the sedan. There are two harnesses at the amp, input and output. The A harness is the input into the amp and the B harness is the output to the speakers. The A harness has all the pre-amp level speaker outputs from the head unit including the subwoofer and amp turn-on remote wire. You can buy RCA plug adapters so you can splice into the factory speaker + and - wires to convert them to RCA plugs for the amp. The B harness has all the wiring to the speakers so you can splice into those wires to connect to the outputs on the aftermarket amp to use the existing speaker wires for your new speakers. You can run a new line to your aftermarket sub in the trunk. Run an amp wiring kit for power to the battery and ground to the frame. The JL Audio amps are perfect for the Hondas because they accept differential balanced outputs. The XD700/5 amp is small enough to fit under the front passenger seat. It worked perfectly to have the JL amp take the place of the factory amp, and run all new speakers. Hope that helps you with your install.