From what I understand, picking up a bunny by the skin on the back of their neck or by their ears is bad for them. I have seen breeders and show judges do it, but I have read that it isn't good for them so I would never do it. Most rabbits don't like to be picked up no matter how you do it since they are prey animals and think they're going to get eaten if they get picked up by something bigger than them.
If your bunny is small, you can use two hands under their ribs/belly like you have been, but a bigger rabbit will need a hand under their back feet too so they feel secure. Two of my bunnies are little and if I try to support their back feet as I pick them up, they hop right out of my grip. I have to put two hands under their ribs to get a good grip on them and then pull them in close and support their back legs. As soon as you pick up your bunny, you should hold it close to your body to help it feel safe.