Ok, so as pathetic as it sounds, the first week or so that we had Miles, we put him in his crate, and slept right next to it, on the floor, so he could see us and know he wasn't being abandoned. After a week I then moved onto the couch next to his crate. And about a month later I was able to sleep in my own bed again!
I was just tired of the sleepless nights!
Whatever you do, don't pay attention to Valis when he is crying. Only let him out of the crate when he is quiet. Even if it's only for a few seconds. It doesn't hurt him to cry. I think all puppies do it for the first week or so at least. Then, they begin to learn,it's their safe place.
I'm not sure about the pottying in the crate thing though. How much room does he have in there? If he has TOO much room, he will do that. He should be able to sit, stand, and turn around in it. Not much else. We always kept a divider in Miles' crate until he got bigger and he never had an accident (except one time when he was VERY sick.)
Here's to a sleepFUL day four!