There was an earlier post about this. Seems like most of the regular posters on here go by total carbs. I personally go by net carbs, as I feel it works for me, but I suspect I may go to total carbs once I find at what point I stop being in ketosis.

Also, MFP won't log your net carbs unless you change the setting for it.

It depends.
Sugar alcohols, in which Atkins bars are heavy, don't always just run through you like they say. For example, sucrose is a 100 on the GI index. Maltitol is between 48 and 35 depending on its form. So that means it does indeed have some affect on blood glucose.
So generally, with something that's carbs are heavy in sugar alcohols, I'd plan on counting half of the sugar alcohol count.
Most people can get away with subtracting fiber carbs without trouble. However, like with anything else, YMMV. There are some people so carb sensitive their bodies still react to the fiber.

Read through this really quick. It touches all the bases.
http://community.myfitnesspal.com/en/discussion/10057456/so-which-is-it-total-carbs-or-net-carbs

Your Mileage May Vary

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