I'm new to Atkins, but am quite experienced with food diaries.
What suprised, and perhaps confused me the lost on the Atkins method was this "net carbs" concept. I think this originates because in the USA they show fibre as part of the total carb content (which it's not of course), making for a very confusing situation.
I found that both of my usual tracking apps: LiveStrong and ShapeUp are just not quitable for tracking an Atkins diet. So I found another: Low Carb Diet Assistant, that seems to do the trick.