Congrats on the new puppy. How old is she? I didnt have much problems with Gucci barking or whining, i guess i was lucky. I didnt crate it her either. Thw first couple of months she was kept at nite on a hallway that I have enclosed with 2 baby gates and lead to the bathroom. So she had acces to the bathroom and the hallway, There she had her bed, water, toys and the pee pads that I had in the bathroom. Anyway, I herad here that you can tell her " No", in a stern voice and ignore her and she will get it eventually. Also you can buy this a snuggler. Is like a stuff animal that has like a build in clock or something similar to simualte the pups mom.
http://www.snuggleme.com/puppies.html
Good luck. Hopefully others have better advise.