Fat burning question?

I'm currently trying to both get in good shape and build muscle but I have some belly fat I would like to get rid of. My current weight lifting regimen is 3 days a week upper body including abs and 3 days a week lower body. This amounts to 5-6 hours of intense weightlifting a week and I have good nutrition(low fat high protein and carbs) and I can tell that I am building muscle. However, my cardio is pretty bad(I can run 1.5-2 miles before I need to quit) and I want to improve it. I know that when you run on an empty stomach your body uses your fat stores. So, my question is, when I run on an empty stomach, will my body go for my fat stores or will it go for the muscle that I am building?