Setting or Resetting a Toilet

From Stephen Hallo III, former About.com Guide

With the flange cleaned off you're ready to put the new wax down. If it's cold outside, it's a good idea to put the wax on the dashboard on the ride home. Warm wax will make a much better seal. If your flange is far from the floor you may need to put a riser ring in to make up the difference. You can also use a flange-free wax ring on top of the other ring. If you are replacing the closet bolts, now is the time you want to set them into the floor flange. Use a washer and nut to tighten them down onto the floor. Make sure that they are even so that your toilet sits straight when you go to tighten it down.