Refined carbs are the enemy. They provide nothing but calories and a blood sugar surge.
If you don't want to drastically cut carbs long term, you might want to try South Beach. It focuses on healthy eating with good carbs. When you first start out you can't have breads, rice, fruit, or some vegetables, but that phase lasts only 2 weeks, then you start adding back in the things you couldn't have the first two weeks and seeing how they affect you.
For a comparison between Atkins and South Beach, please look at this link:
http://www.3fatchicks.com/forum/showthread.php?t=92524
I don't know much about Atkins, only enough to know I can't do it. But I thought telling you about South Beach might give you some more options. I'm on it because of high triglycerides and insulin resistance, and I need to control the amount and type of carbs I consume.
Good luck whatever you choose. And I'm sure someone else will be able to tell you about other programs that might work for what you are looking for. I pretty much only know what hasn't worked for me, and a little about things I thought about trying.