The only reason it matters is your taste preference. While dark sugar has more molasses, thus is a little more acidic and a little more hygroscopic (meaning it holds more moisture), you'll have slightly fluffier, slightly moister cookies, especially if you have baking soda in the recipe. But the only real change is in the depth of the toffee caramel tones in the final product. I prefer dark brown sugar in just about everything I make, so I make my brown sugar a little heavy on the molasses.