if sydney is between 3-5lbs right now. 1 cup of natural choice should be about right. i've never had bunjee on natural choice, but he does like the sample package of ultra puppy food i got. and yeah, they eat less of the premium puppy food because it's no fillers and more nutrients. you should see less stool too. it's good that you took her off puppy chow and onto something better.
if your vet says sydney is healthy then i wouldn't worry about and just continue to feed per the feeding guideline. you can see the feeding guideline here:
http://www.nutroproducts.com/ncdogpuppy.asp#feeding