I think what you're doing sounds pretty good. Remember...he's just a puppy and puppies have accidents. They are most certainly not trained overnight, and yorkies can be notoriously difficult to housebreak. I know many people who were still working on housebreaking at 9months-1year old.
If you let him out of his pen, make sure that you can watch him. If you can't watch right over him, put him back in his pen cause he will undoubtedly go potty on the floor when you aren't looking.
Hope this helps!
