Pop the reservoir cap before you press the pistons back in. Most people use one of the old pads to place on the piston while pushing it in to prevent damage. Use decent pads, el cheapos are cheap for a reason. I use Duralast Gold, been awesome for me. And depending on how bad your rotors are, you might be able to just have them turned.
What they didn't mention is if you have a 2wd truck you are going to have to remove the wheel nut, washers and bearings to replace the rotors. This requires you to re-pack the bearing and I would also replace the races. Many places can turn the rotors while on the truck so you don't have to do all that. If you do have to remove the rotor then you will need to set the wheel nut properly. After the nut is set and the rotor is in place you will need to insert the cotter pin back in the spindle to retain the nut. Hope that helps a little.