I haven't had experience with that exhaust, but I can however help you with your warranty question. Chrysler cannot deny you any warranty if you have installed aftermarket parts. They will only not warranty the aftermarket part, which is expected. Provincial and federal laws all state that no company may deny warranty based on any installed aftermarket accessory and/or part unless it has been proven that said part has caused said problem. If you are ever in a situation where the dealership tries to deny warranty, just let them know that you will be in contact with the BBB (better business bureau) and your lawyer. That will make them rethink trying to pull one on you. Good luck on your install and happy jeepin'!
P.S. Most cat-back installs are simple. Check to see if this one is listed as "bolt-on". If so, that means you just need to use a saw-all on the factory exhaust just behind the factory cat and then rest uses u-bolt clamps. While you're at it, get a high-flow cat, you'll notice actually performance and milage difference with one. Magna Flow makes both a bolt-on and a universal fit that will work.