I think it is really hard to train a dog, especially a Yorkie, to accept sleeping in bed with you some nights, and sleeping in the crate others. Sounds like she prefers being with you. It's the Yorkie way.
Max slept in his doggy bed in his xpen next to my bed his first year. His choice. Then he started sleeping with me. He is now 7 years old and often goes to his doggy bed because I move around too much or he gets hot.
I think most dogs will sleep longer at night if they are near their humans.
Potty: are you doing strict outdoor training, or using pads too? My boys have pads available, so they pee when they need to and don't wake me up. They will wake me up to poop because they want that taken care of right away.