Put the food down for 15 minutes then take it away. Do NOT leave it out for her to pick at until the next feeding. There are two reasons for this. The first is you want to know exactly how much she is really eating at each feeding. The second is by removing her access to food in between feedings you will teach her to eat when food is offered because food won't be available whenever she wants it.
As for her thinnning out, my puppy boy is going to be 17 weeks old on Thursday and is a bit skinny this week since he had a growth spurt. Puppies tend to go through cycles of just a little pudgy, just right, a bit skinny and back again as they grow and their calorie demands flux depending on the amount of growth.