Not to get too detailed but I am a certified personal trainer and got into running a little over a year ago (Completed Marine Corps Marathon), although I have always been a fitness guy.
Running in the morning before you eat is the best time to run if you are trying to lose weight and prepare yourself for a race/training that is in the morning. If you start getting up above 10 miles or so, you will have to eat or you will "bonk"/hit the wall. If you run late in the afternoon, try not to eat 2 hours prior to running. If you get up to 15 - 20 miles on a long run, you may have to do number 2 before it is over...trust me. It is a common/weird phenomena with long distance runners.