I updated the Angry Chipmunks tutorial with a nicer way to synchronize the bodies and sprites. It has a subclass of ChipmunkBody that you can add a list of CCNode objects to. When Chipmunk updates the position of the body, it will update the sprite for you too. No need to store the lists yourself or run synchronize the positions anywhere in your own code.
You can download the new Angry Chipmunks code:
http://chipmunk-physics.net/downloads.php