I'm not sure running on an empty stomach in the morning is a bad thing.  I suppose it depends how far you're going and how hard you push.  If you don't run hard you could probably get away with a bagel or bowl of oat meal.  Side stitches (cramps) kick in if you run hard too soon after eating.

Anyway, if you eat after your run you should be fine.  If you're trying to lose weight, you just need to burn more calories than you take in.  Here's a nifty little calculator that'll tell you what you're burning for calories.. http://www.coolrunning.com/engine/4/4_1/94.shtml

I'm trying to drop 10 pounds and this little calculator helps a lot.

Good luck!

Running on an empty stomach is not a bad thing. When I started running, i would always, and still run on an empty stomach. Although, i do take slow digesting protein the night before, and it's fuel for the next morning. But as long as you're hydrated, that's most important.

As long as you don't sacrifice performance and have no adverse GI symptoms you should be fine. Your post workout meal even if you are trying to lose weight should be 3 or 4 to 1 carbohydrate to protein ratio with little fat within an hour for maximum recovery. For weight loss don't eat more calories in this meal than you just burned. For weight loss with activity keep your calories at about 10 per pound of body weight.

Personal Trainer Los Angeles