It will take a few nights for your puppy to start feeling comfortable!!! I really like the idea of crating, I have always starting crating my dogs until they are old enough. It gives them a safe spot and a home to feel comfortable. With my most recent puppy, he was pretty bad so I talked to the breeder. She told me to put some blankets in the bottom of the crate and under the blankets put a small ticking clock. This mimics the sound of a heart beat and will be reassuring to the puppy. Maybe even put a stuffed animal in the crate with it that it can curl up with, it's probably not used to not having litter mates to cuddle with just yet!!
Good luck, and know he will quit eventually. He just needs to feel safe!