Maddie went through this phase...she was very skinny (and still is really) from 6 months on. She has never been a big eater though...and FULL of energy...so she just burns off the calories.
My vet told me that scheduled feedings actually help them to GAIN weight....instead of just free feeding (leaving it out all the time). That's because the more active pups tend to run by every once in awhile to grab a bite and then keep playing (just eating a little at a time) and that causes them to burn everything off. But if you feed them a "meal" at breakfast, lunch, and dinner they eat more at a time. Just like when humans need to lose weight they are told to eat several small meals instead of a few big ones.
Also, I agree about the Science Diet...it's a horrible food. I suggest Innova because that's the only dry food Maddie, my pickiest eater, will take. If you put that stuff in front of her she'll gobble up the whole bowl!
And of course, with Maddie, I sneak her extra treats and give her canned food every other day to try and fatten her up. She FINALLY has a little belly after struggling with her from the time she was 7 weeks old!