Something I use for carb counting is Corinne Netzer's Complete Book of Food Counts. It's small enough to take with me anywhere and is especially handy when I'm somewhere without a computer and need to know how many carbs are in something. It also lists practically every food you could think of eating including entries for foods at many fast food restaurants. The book costs $7.50 and is the size of a thick paperback book.
I think the difference between the counts on Dr. Atkins' site and Fitday is that the counts on the Atkins site already have the fiber deducted and those on Fitday don't (you have to deduct the fiber yourself).