I still can't find the excellent article I read last year, but some of the science is in this one
As I understand it (disclaimer I am not a scientist, but as I have a child with type 1 diabetes I know a bit about carbs, blood sugars and glycogen, and I read widely last year when marathon training)...your muscles need ADP to work. They get the ADP by converting ATP + creatine + oxygen into APD, which is why you need to breathe more heavily when you start to run. This is aerobic exercise.
You get your ATP source from gylcogen, which is stored in muscles and the liver. Most of us can store up to about 2000 calories-worth of glycogen.
After than you start to burn fat. Your body will always use the most easily available energy source. Burning fat is harder, and uses more energy, which is why you feel rubbish when you start to burn fat (and why marathon training involves long runs, so you can get used to burning fat). Gels are supposed to stop you hitting the wall because they are more easily convertible to energy than fat, so in theory you shouldn't reach that stage if you use gels.