I'm not a physical trainer, but I can give you a general answer. I wish there was a way to be simpler, in my response... but the truth is that science has not yet uncovered the secrets of how our bodies function. On top of that, this is a pretty complicated topic. It's basically molecular biology.
Your body has three major energy systems. The type of system used is determined by the type of work the body is doing. Food in your stomach doesn't get used as energy until it's broken down, and makes its way into your blood stream. Not much of that even happens in your stomach. Most of it occurs in your small intestines. Protein powders, BCAA powder, and other fast absorbing drinks, don't enter the blood for as much as 20+minutes (at least that's a good rule of thumb). Stored fat doesn't get used as energy, until your liver breaks it down into its component compounds, and it reaches your blood.
So the answer is... not food in your stomach, or stored fat. The only preference your body has, is for whatever is most readily available. This is determined by the timing between eating, and working out, and also the composition of what you've eaten, the type of work being done (think endurance running, VS heavy weight lifting), and the intensity, and volume of that work.