You might also try to 'smaller up' his crate space...leave him just sleeping room and potty space with a potty pad where he can go if need be....and expanding it as he grows. At 12 weeks old, he is still pretty young...you want him to be able to stay clean, have both areas (sleeping and potty) at his disposal, and not become distressed over bodily functions he may not be mature enough to control while you work on training him in the way you'd 'like him to become'...
He is definitely a cutie pie, though, and not only will he steal your heart, he will be your very devoted constant companion most likely. Just hang in there!