We crate trained both our females, and I am not sure about males so this may be irrelevant.
The advice given to us was to stuff something in the crate. A towel, a blanket, just something to make the area they are in smaller so they have no room to turn around and circle before they pee. I think it goes along the lines of a dog won't pee where it sleeps and if the area is just big enough for him/her to sleep in they won't have the room to pee.
Hopefully you work it out and make sure you clean the crate out with a good enzyme cleaner after every pee. If they smell it, they will probably go there again.
Don't get too frustrated! He is just a baby still and has a lot to learn and a lot of bad habits to break, and good ones to pick up. I know crate training ours took tons and tons of time and patience. The end result is worth it. Don't ever scold your dog for accidents unless you catch him in the act. And tons of love and positive reinforcement when he does it right.
My girl even pees on command. "Bitsy, go pee!" and she drops her little butt and lets it go. I think only females can do this, though. It is a great party trick.
