Harriett is dead on with the statement that CF is a "spectrum disease" -- there are HUGE variations in severity and age of onset for symptoms. That said, "atypical" is usually used to distinguish from "classic" CF. The biggest factors in a doctor's decision to label someone "atypical" seem to be: 1) age of diagnosis (anything after about 10 seems to get you the atypical label), 2) mutations (rare or more mild mutations), 3) pancreatic sufficiency, 4) borderline or negative sweat test numbers, and 5) milder pulmonary symptoms. I would say if someone meets at least two or three of the above criteria, they are likely to be labeled "atypical" by some members of the medical/CF community, for better or for worse.
There are many "classic" CFers who manage to maintain good lung function until much later in life, but if you're diagnosed in infancy/young childhood, have higher sweat test numbers, and are pancreatic insufficient, no one is likely to call you atypical regardless of your lung health.
I personally have mixed feelings about the whole thing. I don't think the labels are very helpful, but then again I'm a "two severe mutations, diagnosed at 6 weeks, pancreatic insufficient, sweat test of over 100, PA-culturing" style "classic" CFer, so I've never had to think much about the atypical designation and what it means.