Definately wax on flange first. Ignore the box instructions. Like anyone reads instructions anyway

Wax won't stick to wet surfaces. Make sure everything is dry. Set toilet first without wax and see how much wobble is there and shim accordingly. Lift toilet back up and leave shims in place. Place wax on flange. Take MEASUREMENTS. You want at least 1/4", 3/8" of wax smash. More is ok if it doesn't restrict bowl hole. If set on ceramic or concrete, glue that sucker to the floor (sealer of some sort around the bowl edge) Remember, wax only smashes once, if the toilet moves it will leak. The MOST important part of a toilet setting is MAKE SURE IT DOESN'T MOVE when you're done. No wiggle, no wobble. Done deal.
Don't worry, there will be other things to fix in the house down the road. Guess who they'll call..........the guy who finally fixed the crapper