My little Mouse is skinny, and has always been skinny. I have a real hard time keeping weight on her. She is not a little puppy anymore, and is definately NOT a pickey eater, she will eat whatever I put down for her, however, I have kept her intact as the worst thing you can do for a Doxie is let them get overweight, even the slightest extra weight is detrimental to their backs. So her metabolism is very high, and I keep her food intake strictly monitered, as she gets little in the way of walking due to missing half a foot.
I would keep him on TOTW, (It's an EXCELLENT food!) but switch to their canned formula, or mix it with kibble until he's eating a bit better. Talk to the vet and get his opinion, but you should be able to feel the ribs easily, without them being visable, and the hipbones and spine should not stick out... However that's for an adult dog, young puppies are often "bony" so I expect he's within proper conditioning.