When it comes to counting calories.... Calories are just that, calories.
You can eat two twinkies and have 600 calories
or you can eat a chicken breast salad and have 600 calories
Calories are calories. Yes you may obtain your calories in the twinkies from sugar and corn syrup, but they are still calories. Your body will still burn them. You may not feel as good, but in the end calories are calories.
Something I Like about a program or app for counting calories (I use myfitnesspal now, but have previously used others including one by livestrong.com) is that in addition to calories, the program keeps track of carb/fat/protein as well as vitamins and minerals and grams or sugar etc. so it becomes easier to see where your calories are coming from (I.e. if they are all coming from fat or sugar, which is something I try to avoid)...