Typically, it should help you lose weight. Dr. Atkins said in his book, Dr. Atkins' New Diet Revolution, that exercise is non-negotiable when trying to lose weight on his low-carb diet. Exercise should raise the metabolism when eating fewer calories would make it do a nose dive.
However, it is clear that some people like Dr. Taubes, author of Good Calories, Bad Calories, do not think exercise is beneficial in weight loss. Certainly in Africa where people walk miles, many of the people are still obese. Why? Besides living off carbs, there is another reason and I think Dr. Jonny Bowden hits the nail on the head when he says that some people will compensate for exercising by eating more. This article is very interesting!