OK I see where you are confused. If you eat too much of anything it will turn eventually into fat, unless you are burning it off through exercise.
Your body prefers to digest and burn carbs for energy as they are easier to break down (into monosaccharides, simple sugars), we learned that in biology at school. It's very simple to eat too many carbs, as they are quite addictive and found in things like cakes, biscuits, chocolate and all those yummy things that are so morning. This produces too much sugar in the blood stream with all the risks that implies.
Now if you limit the carbs the body will have to use fats and proteins as its primary energy source. Firstly, these take much longer to break down into energy, and the body has to work harder to do this. Also these foods can make you feel full for longer so you have less urge to snack or over indulge.
That's probably over simplified but my undetstanding of how it works.