Welcome to YT! I don't think you can overfeed a puppy. That is my belief. I free feed puppies. If you are concerned with Roxy's weight though, just have a vet give you his/her opinion. Basically, if you can still feel the ribs well, she's not fat. She's just going to be on the larger side of the Yorkie spectrum. This is a good thing.
For the dry flakes, make sure you are rinsing her well when bathed. I know that sounds silly to say but seriously..I have learned that when I think I'm done rinsing...I rinse for a few more minutes. Other than that, she may have dry skin. Try adding about 1/8 tsp of organic coconut oil (I use nutivia) to her food. You can rub it directly on her tummy area too. My Mandie has dry skin and tends to have dry hair so I do this. I actually, also, brush her teeth with the coconut oil..she loves it.