Help him relax when he comes home. When your puppy gets home, give him a warm hot water bottle and put a ticking clock near his sleeping area. This imitates the heat and heartbeat of his litter mates and will soothe him in his new environment. This may be even more important for a new dog from a busy, loud shelter who's had a rough time early on. Whatever you can do to help him get comfortable in his new home will be good for both of you.
Submissive urination is a normal way for your puppy to demonstrate submissive behavior. Even a dog that is otherwise housetrained may leave dribbles and puddles of urine at your feet when greeting you. Excitement urination with a puppy is usually caused by lack of bladder control. The puppy is not aware that he is urinating; he's just excited and any punishment will only confuse him.