Crate training is great.
You may try distraction to stop the whinning. Put a few pennies in an empty soda can, tape it shut and shake it whenever they whine, it hurts their ears and they will learn from distraction, not to whine. But they also grow out of it. Just don't give in, give them time to learn the crate is a safe place.
And I would not put anything in the crate with the dog at first, esp if you are still house training them.
Just remember like everyone said it should not be used for long periods of time. Ours liked their crates, because they could be near us and see us, while they learned their crate was their den.
What kind of puppy did you get?