Crate Training

So I did some research because we are having a hard time with the crate training for our puppy. She will cry and yelp for a long time while in the crate. I am realizing she is having separation anxiety. It makes me feel really bad. I don't want her to feel scared and alone. I have realized that she is seeing her crate as punishment which is not what we want her to feel. I am going to have to rework our training process. She is very good at bathroom control etc. She will sit at the door and whimper when she has to go out. Not to say she has not had a few accidents, she doesn't' have bladder control yet because she is only 8 weeks old. She also knows what "sit" means. I didn't teach this to her either. The first day I had her I went to put the leash on her and said sit and she did. She is a really sweet puppy and she desperately needs a name or she is going to think her name is "Puppy"