In some situations the toilet may have been seated on two stacked wax rings, one with a flange and another without a flange. This arrangement is sometimes necessary because of a thick floor covering, recessed toilet flange or other unique situations. Doubling the wax ring slightly increases the risk of a leak, so take care to align them and press them together to ensure a complete seal.
Take the new wax ring out of its package and remove any protective film or covering. Center the ring over the drain port on the toilet bowl and press it firmly in place; the wax side seals to the toilet and the plastic horn, if any, fits into the floor flange. It is important for the wax ring to make a tight seal with the toilet.
The bottom of the toilet should not sit directly on the floor. Instead it should sit on a bead of plumbers putty all the way around its perimeter. Take a large glob of putty and roll it between your hands to make a long round strip about a quarter of an inch in diameter. Roll out enough to cover the entire perimeter. Place the putty along the raised ridge that will contact the ground and press it so it stays in place while reseating the toilet.
Check that the flange bolts are still in place in the toilet flange. The new wax ring may cause the toilet to be taller than before and thus the bolts may be too short. However, as you press down on the toilet, the wax ring will reshape to make a seal with the floor. Make sure the bolts are aligned with the holes in the toilet bowl before pressing down on the bowl. If necessary, you can replace the flange bolts with longer ones and then hack saw off any excess after you've completed the installation.