Kristen,
I totally understand what you are talking about. When I first started Atkins in August I thought I just count the carbs, period. I didn't find in the book that I was to count the net carbs only. In his list of foods and carbs the fiber isn't taken out or mentioned, at least in the 2002 book I had from the library. So here I was eating only 20 or most days less than 20 carbs period a day. I lost like crazy. I was really happy about that. BUT, I was not feeling like I was eating enough of the "good" stuff, veggies and such. I was skimping on the veggies and using my carbs on stuff like heavy cream for my coffee, eggs, cheese, and splenda. Now that I have started counting my carbs and fiber on fit day I am able to work in more veggies and feel safe doing it.
I am starting with a whole new problem myself and that is I have started owl and in just the last couple of days let myself count too many "sweets", legal of course, as quite a bit of my carb total for the day. I was enjoying too many cheese clouds, and crustless keylime pies and such. I am going to get a handle on that this week! I have to. I refuse to let myself get back into the habit of poor eating. I need to take care of myself for me and my family.
I wish you luck. I hope you find a happy place that works for you.