Replacing the Pads
Before you race through putting everything back together, look in the box your new pads came in for a small tube of brake lube. The brake lube is provided for the caliper mounting bolts. Clean the bolts off with your brake cleaner and lube them up lightly with the brake lube. The lube is important as the caliper is allowed to move on the mounting bolts as the pads wear. You may also want to coat the backs of the pads with Disc Brake Quiet or similar product before you install them. This will help eliminate any squeaking that may come from small vibrations between the pad and the caliper. Do not put in on the braking surface.
When reinstalling the caliper, remember that the bottom edge of the pads are notched and make sure they sit properly on that ledge. Place that bottom edge first and rotate the top into place. Be careful of the rubber boot around the mounting bolts. Don't let it get crushed or torn. And, while you're there with the wheel off, it is really easy to grease that upper ball joint.
The caliper is still attached to your Jeep by the brake fluid line, so be careful turning it over to remove the pads. Before I remove the pads, I use a hand clamp to compress the caliper completely to make room for the new thicker pads. You may want to keep an eye on the fluid reservoir while you compress the caliper piston back as it pushes fluid back into the reservoir. You don't want it to overflow and make a mess. You can use a clamp on the inside portion and in the center of the inner pad. Pushing on the center of the inner pad applies the opposite force to the the caliper's braking force.
With the brakes removed there is nothing holding the rotor in place except maybe some dirt and rust. Now is a good time to pull it off to inspect it, and get out your can of brake cleaner. Give the caliper a good cleaning and clean up all the brake dust before you install new pads and start to reassemble everything. The rotor surfce should be smooth and flat on both sides. If yours has grooves it should be fixed or replaced. A reputable brake shop can turn your rotors on a brake lathe, but there is a minimum thickness required. If they have been scored too deeply or turned once already, you may have to replace them.