And the stored calories, like body fat and glycogen? What side of the equation are those on? And the energy needed to convert complex carbs and protein into glycogen? The energy used converting glycogen to ATP?

If you can demonstrate everywhere the energy comes from and everywhere it goes and where and how it's used in the body, I imagine there's a nobel prize in it for you. There's still a lot we don't know about where all that energy comes from and goes.