Whey is a good choice if he tolerates dairy, but what do you mean you bought shakes? Did you buy powder, or something liquid? What's the nutrition data and ingredient list?
1/2 an hour 2 days a week probably isn't enough to maximize his progress. He will probably benefit best from about 3 days a week of progressive compound lifts with a barbell. The trainer should teach him to squat, deadlift, standing press, bench press, and power clean, and then you won't need to pay him any more (assuming your son is mathematically capable of adding 5 to other numbers all by himself).
Save the money you're spending on a trainer and buy him a copy of Starting Strength, Basic Barbell Training, 3rd Edition by Mark Rippetoe. And let him eat.