This is what my dad told me to do when I got my dog, and he's used on every dog he's ever had, and had very good succcess with. Pretty much for the first few weeks you have your dog it has to live in the crate. Take it out every 1-2 hours, and if it goes to the bathroom let it stay out of the crate for approx. 30 minutes. Play with it etc, then you put it back in the crate. If not, when you come back inside back to the crate. Don't use it for punishment, and like you said, it won't go to the bathroom in it's "den" aka the crate. If it is, you need a smaller crate. Give it a treat when you put it back in the crate, after the 30 minutes, rinse and repeat. You will have to deal with it barking and whining while its in the crate, a good way to help reduce the barking etc is to put the crate in the same room you will be in where it can see you. It took my dog about a week to learn outside is where he uses the bathroom, when I do this, I don't have to go in the crate. I know it seems kind of harsh, but it works.
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