Dogs need to be with their pack (family) now that you are his pack leader. He is barking out of fear of being alone and because he needs to feel secure. If left alone too often and for long periods of time he will build up anxiety that can eventually turn into a serious issue. I would suggest taking his cage into the same room as the family is in. If its time for a nap than just place a light weight blanket/sheet over the top and as long as he can feel your presence and hear your voice it will help sooth him and he will calm down. You are welcome to view my site and go over some of my tips for raising puppies. these are all things that I have use with my own crew or four Yorkies. They do work if you have the time and patience to work with him. Hopefully you will find something that works for you.
You can find it here:
www.dawnsyorkies.weebly.com/trainingtips
Plus you need to be sure that those bark are not cry for a potty break ! Potty training is a very tough thing to accomplish and its best not to get him started peeing in his cage.