With all my guys, I usually sit on my bed cross legged and then lay them with their head in the crook of my elbow. To keep from kicking/turning over, I find if you firmly hold them against you, and even hold their back feet steady, they won't have enough powerto be able to kick.
You can also try the method I use with Jasmine, my girl who gets terrified when she's flipped on her back. I put her on a towel on the deep freeze, and lean gently on her to make sure she can't rear up. Then I have one arm around the front of her so she can't jump forward and then my other armcurled around her back end (so she can't back up), then hold the paws with one hand a clip with the other. Then I just turn her around, and do the other side. Although she is pretty calm and sits still, so might be a problem if your bunny is hyper!
If all else fails, wearing a couple of long sleeved shirts and a thick sweatshirt is always good to avoid scratches!