I have no experience feeding puppies raw. But I think I would definitely leave kibble down all day for him. He is a growing boy!
Once he gets older, then you can keep track if he's over-eating. Because some pups WILL over-eat, whereas some self-regulate pretty good. But I wouldn't really worry about a 12 week old pup being overweight or anything. So for now, I'd just keep doing what you're doing!