Carbohydrates: Muscles and liver
Fats: Adipose (fat) tissue
Protein: Used quickly, not stored long term as an energy source
All three substrates are used during exercise. Depending on exercise demands and current nutrition levels, the body uses these different energy sources to maintain enough energy to complete the work load. Fat provides the highest number of adenosine triphosphate (ATP) enzymes for energy, but it must be broken down before it can be utilized. Carbohydrates are quickly available in the muscles and liver to be utilized as ATP. Protein is the least efficient means of creating energy and provides only 5 to 10% of energy needs during exercise.
The most efficient way to use substrates is to maintain a healthy diet, drink plenty of water, and exercise.
Wilmore, Costill, Kenney. Physiology of Sport and Exercise (Fourth Edition), Chapter 2