This is a really confusing question/scenario. I'm not altogether sure exactly what you're asking. About glycogen: your *glycogen* is not depleted in the morning, especially if you had carbohydrates the night before, although *blood glucose* will be low. Glycogen is glucose stored in the muscles and gets low through activity. Blood sugar is readily available energy, which if there is no immediate demand for energy will be stored as glucose or possibly fat if glycogen stores are full.
If that doesn't help answer your question, try rephrasing it a little more succinctly if you can. Please.