I’m pretty sure picking a bun up by the neck is not safe for the bun, they could seriously injure themselves. They tend to get frightened with being lifted off the ground because they are prey animals. The best way is similar to what it sounds like you are doing, but I’m not quite sure what you mean. Support the bun’s chest with one hand and (ESPECIALLY) his back end with the other. It’s is more secure this way if he tries to kick away. A bun can really hurt itself kicking in the air, they are really powerful. Another way to carry him (once you’ve picked him up) would be to hold him with all four paws on your chest his head close to your shoulder, one hand supporting his bum the other on his back. This is how my bun likes to be carried. I can pick her up the first way described but she is still fearful, I think because they like to have all four feet touching something solid. Hiding his eyes as you’re caring him might also help with him being frightened. I hope this helps a little bit. More people will probably be along to help out if I was confusing hehe.
If you have an extremely scared bun who tries to bite you everytime I think the best way would be to use a towel or blanket to help you. Take the towel and put it over the bun (covering his eyes with the towel might help here too) and as you scoop him up wrap him up in the towel and hold him like I said before against your chest supporting his bum. Another tip is when putting him down to stop him from falling or trying to kick away. Get down on your knees and lower him from there. It is a lot small of a drop if he does manage to get away and less scary for him
Also don’t get discouraged alot of rabbits never like being picked up or carried. It’s just not in their nature to feel safe when this is happening. However when you’re down on their level or on a couch they can still be affectionate because they feel safe. Others are just never “cuddly”
Anyways hope this helps!