I understand your concern and your puppy's. If your worried about him peeing on your bed why not crate train him so that he can sleep upstairs with the rest of the family. He might do better because he will be able to see everyone and won't feel so alone. I went through the same thing when I first got my lil girl Hershie.
She didn't like the fact that she was left all alone when she knew were were all in another room when she knew someone was awake. When I moved her crate into my bedroom, she did alot better and I didn't have anymore problems with her barking for attention. I never had a problem with her getting to sleep or even staying asleep while we were all in bed but when someone was up she wanted to know what was going on and it sounds as if your baby is the same way.
