Yeah, I have similar issues with Wingnut (4 month old Military Macaw). He is VERY beaky. Usually not real biting. Very rarely would he actually chomp. He does everything short of actual aggravated assault though. When he steps up, more often than not, he will involve his beak some how. When i ask him to step up off the top of his cage, he will often get real vocal, and lunge.When I pull him in close, and he is nestled in the crook of my arm, for scritches, his new thing is to nibble on my shirt, or my skin, which is like a pinch, and I have to stop him.
I can usually just handle his beak, and direct him elsewhere. If it gets a little out of hand, I pick up a target stick, and start clicker training, which distracts him, and settles him down.
To be honest, I don't know if I'm doing the right thing, it just works for us.