I've done it both ways with equally good results. As long as you have a wax ring that is thick enough to be compressed when you set the toilet in place, you should be fine. It's good to have a helper to assist in aligning it when you lower the toilet the last couple of inches. Sometimes, even when I have a helper, I mark the position of the toilet before I remove it by putting several pieces of masking tape along the bottom, outside edge of the toilet and on the floor, and then make alignment marks on them with a colored marker. This helps you guide it back in for a good "landing" and is useful in aligning so you can match the bolt holes with the bolts without knocking them out of position.

Kudzu's right about the tape being helpful. Also, if you're doing it yourself, another trick is to place a 2" or so piece of plastic straw over one of the hold-down bolts (which should be locked in place with the extra plastic washer or a piece of wax. That helps to align the toilet one bolt at a time, as opposed to both at the same time (do the taller one with the straw first). Once down, remove the straw.

Most plumbers put the wax on the floor flange.

I've seen a few jobs where someone put the wax on the bowl, walked the bowl over to the flange, the wax falls off, and plop! Lands blocking the drain.

For that reason, plumbers place the wax, on the floor flange.

Unless the flange is above the finished floor, you will need two wax rings.
Most homes in the Seattle area are installed with two wax rings.
If the "add-on" flooring is cut around the flange, you most likely are looking at two wax rings.
Terry Love

The toilets i buy come with an extra set of nuts. I place the bolts on the flange and fasten with one set of nuts, place the wax ring and then place the toilet and fasten with the second set of nuts.

I thought you weren't supposed to stack wax rings?

Although it is a common "Jury rig" fix, Code does not permit the use of two wax rings. In fact, the double thick wax rings we commonly find in hardware and home supply stores are not code approved.

Per Code, the underside of the closet flange is to be in firm contact with the finished floor, which then leaves the top of the flange extended about 3/8" above the finished floor (The thickness of the flange itself.)

The concern here is that if the wax seal is too thick, if it becomes necessary to plunge the watercloset there would be a very high risk of the plunging action blowing out the wax seal.In instances such as when additional subfloor material or ceramic tile is built up on the existing floor, leaving the flange flush with or recessed below the finished floor level, the proper solution is to:
1.Reposition the closet flange
2.Add a "Build up flange" to extend the top surface of the flange up to the prescribed level.

Also, if you're doing it yourself, another trick is to place a 2" or so piece of plastic straw over one of the hold-down bolts (which should be locked in place with the extra plastic washer or a piece of wax. That helps to align the toilet one bolt at a time, as opposed to both at the same time (do the taller one with the straw first). Once down, remove the straw.

The large, green straws from Starbucks are the perfect size for toilet bolt alignment. ;-)