I don't know anything about the Atkins diet, but I do know that for endurance sports such as cycling, higher carbohydrates than protein is the usual diet.

As Velocipedio pointed out they should be complex carbs, which come from pasta, bread (whole wheat) etc, not simple carbs as you get from fruit.

In general, just eat a healthy diet with a good balance of food groups, just don't eat too much of it, and your exercise will take care of the weight.

Good luck, you've made a good start!