I'm sure everyone does it differently depending on their rabbits, with Barney I put one hand under his chest and one under the bum, then lift him, with his back against my chest. I raise his bum higher and sort of bend my head over him so I can see his bum, I check its not got any flies or poo or wee on it, then put him down. The whole thing takes about 30 seconds, very quick, as he doesnt like being picked up. At first he hated it but now he knows he'll be back on the floor very soon so lets me.
Annabelle however hates being touched. I dont know why, but shes quite happy around me, but if I touch her she runs off, unless I bribe her with food, then sometimes she tolerates a quick stroke. What I am doing with her is training her to periscope (stand on her back legs) on command. At the moment she does it for treats. This allows me to do a quick check without touching her, however it is nowhere near as good as a full bum check, so I do worry about her. I also have her bum hair trimmed and use fly guard as an extra precaution.
This video explains why to do bum checks, and shows you a very long version of one. Obviously the man is showing the camera, not himself, so its not quite the same as when you would do it, but gives you the idea.
The main thing to remember when you do bum checks, is that you have to not tip them back so far to trance them, as this is a state of terror for bunnies and they will lose confidence in you and see you as a threat.
http://www.youtube.com/watch?v=3FC2TVwgJxo