Exercising below 65% of maximum effort uses mainly fat as fuel. Above this intensity, carbohydrates become increasingly important, and they're used almost exclusively for fuel at extreme exercise intensities.
Swiss researchers found that fat use during exercise is influenced by prior physical activity. Moderately-trained subjects took 2 maximal treadmill tests: 1 to determine maximal oxygen uptake and estimate fat use and the 2nd to determine the effects of prior exercise on fat use. During the 2nd test, subjects exercised on a treadmill for 1 hour at 57% of maximum effort. After a short break, they took the 2nd treadmill test to exhaustion. Fat use was higher when the subjects took the test after the initial 1 hour run. Two-a-day workouts will trigger more fat-burning during the 2nd workout.
(Metabolism Clinical and Experimental, 58: 1778-1786, 2009)