I've never been on Atkins, but I've been on the Zone for about 2 months and found that a few things smoothed my transition into the Zone. For me, it really helps to use a lean protein source and stick with the "preferred" carb sources, e.g. fruits and vegetables. Broccoli, asparagus, spinach, green beans, and tomatoes all worked well for me. If you don't feel like eating several cups of salad, you can always use chick peas, kidney beans, or black beans to make the serving size more manageable. I usually have a serving of fruit at every meal too. I don't like eggs, so I usually have a smoothie (milk, frozen fruit, and whey protein) or oatmeal, cottage cheese, and fruit for breakfast. Over time, you will discover foods that work best for you.
I don't know if this'll help - perhaps the transition from Atkins is completely different than the transition from a higher carb diet.
As I mentionned, I've been on the Zone for 2 months and I am very happy with it so far. I've lost weight and have had lots of physical and mental focus.