What a cutie! Now is a good time to get him used to a dremel. His nails need to be shorter both for his own feet comfort and to keep him from scratching her.
Your Yorkie isn't stupid. She knows she is going to be terribly out-weighed and needs to train him NOW who the boss it. Let her. If he bullies her, remove him consistently so she knows you will help protect her. Limit the time he has access to her and try to make it fun time... treats/training, or simple one on each side getting petting while you watch tv. You want to teach him that she isn't a chew toy and you want to teach her that having another dog doesn't have to be scary.
No matter what you do, she may never want to play with him. Your goal, for now, is to make her feel secure and him to stop being a wild thing.