I suggest you hold off on the yogurt. You want a low calcium diet for your puppy and yogurt has lots of calcium. If you look at adult dog food versus puppy dog food, you will see that puppy formula has lower calcium. Adding yogurt to puppy formula negates the balance.
That said, if your puppy has digestion problems, you can analyze what's causing it... It can be an allergic reaction to the food, stress, parasites, or a specific ingredient in the food that your dog is overloading on. You will need to try to figure out what's wrong.
In any case, unless your puppy is exhibiting nutritional deficiencies, it is best to just go with the dog kibble and training treats until he gets older.