The way that we started with Maci when she was just a little puppy is we would leave dry food down for her all day long. She would eat periodically throughout the day. Then we would add some wet food around lunch and dinner time.
In fact, we still leave dry food down for her all day long now as well. We have found though that she still eats around the same time everyday anyways even with the food left down all day.
As long as your puppy continues to eat each day you shouldn't have any problems at all. He knows when he's hungry and when he's not!