Actually, the civic already comes with 6x9 stock in the rear so it should just be a simple swap. It also comes with 5.25" in the doors and 1" tweeters in the mirror mount. I've been told that to switch to the bigger 6.5" is easy because there is already space in there.
My main concern is the wiring. How do I wire up the crossover? Do I install the new speakers but use the existing wiring? How does introducing the crossover now affect how things get connected together?