I also heard that is wasn't the best idea to have the crate in your bedroom, however sometimes you have to do what you have to do. We've had our Molly for 2 1/2 weeks now and she finally stoped howling at night. How we moved her into our room out of a crate and into a dog bed. The past few nights have been wonderful. She wakes us up generally around 3:00 by whining and we put her out and back to bed. Before that in the crate she would mess herself constantly, she ended up pulling or breaking all her bottom baby teeth chewing on the crate.
We tried everything in the crate, hot water bottle, ticking alarm clock, shirts with our scents on it, filled kongs, toys treats and nothing would stop her. She still won't go downstairs because she knows the crate is still there. We have found she is getting a better sleep and so are we.
So you can try putting the crate in your bedroom maybe just being close to you will give your puppy a little sense of security.