IIRC the bike is supposed to be on the center stand. I use the centerstand method and fill the final drive until I can feel fluid almost getting ready to come out of the hole. Just make sure you don't spin the wheel to get more fluid in, it will just spit it out onto your rear wheel on your next ride.
I haven't found any appreciable difference one way or the other. I drain mine on the centerstand as well. I then moved the rear of the bike downward slowly until the wheel touched the ground. No more came out. As Jeremy states, don't overfill it. I typically leave about a 1/4 inch below the rim but that's just me.