Carl, I form plumber's putty into a rope or string-like shape and put thaton the bottom of the toilet along with the wax ring. That levels out any floor irregularities so that the ceramic is supported all the way around and seals the wax under the toilet. When you sit on the toilet after you put the bottom on the floor, that does make the putty conform. Wax seems to have a way to get out and under the bottom of the toilet if you don't and this is particularly the case on floors with small tiles and lots of grout lines.
I haven't caulked around the toilet bottom, like you would around a tub base.
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