Found this on zoneperfect.com:

Fiber content does not chemically break down into sugar (glucose), so it does not contribute to the overall “sugar load” of the carbohydrate. To calculate the carbohydrate content you take the total carbohydrate grams, subtract the fiber grams, and this will give you the remaining carbohydrate (net) grams that will be broken down into sugar. For example, if a slice of bread has 27 total carbohydrate grams and 3 grams of fiber you have a net carbohydrate content of 24 grams (27 g – 3 grams = 24 grams). This explains why some high fiber foods will have a more favorable impact on the blood sugar and insulin levels.

From this I understand that a higher fiber percentage in the carbohydrates is beneficial to fat loss. My question is, does this also affect how I should calculate my daily protein/fat/carb percentages?

The Atkin's clan calls the net sum of Carbs minus Dietary Fiber as "Impact Carbs". I count carbs as carbs, fiber or not. From what I have found on the net at BB.com, CKD diet boards, and John's own page here, that is what most people do. On the other hand, you need to make sure you get a certain number of grams of dietary fiber and I track that number aside from my carbs.

Your mileage may vary and I hope if I've mis-stated anything that others will let us know.