On My Fitness Pal (MFP), it'll give you a daily calorie amount based on your height, how much you want to lose each week, and whether you are sedentary, lightly active or very active on a daily basis in your job. It is a bit of a blunt instrument and relies a bit on people being sensible with it. A lot of people set it so be losing 2 pounds a week, which unless you are very overweight is probably quite a lot to ask and can limit your calories quite severely. Depending on where you are in the BMI scale you are probably best of setting it to lose between 1/2 pound and 1 pound a week and this'll give you your base calories with the appropriate defecit to lose the pound each week. What MFP expects you to then do, is to log your exercise, and this then calculates a rough calorie burn (or you can enter it from your heart rate monitor). The system that MFP uses expects you to eat those exercise calories in addition to your base calories to keep your calorie defecit constant and so you have enough fuel to power your body if you are doing a fair amount of exercise.
I've used MFP for three or four years. Firstly to lose weight, then to maintain. I don't log every day now, although I did religously for the first couple of years. I lost about 5 stone over the first two years, and have kept if off since.
Slow weight loss is best, especially if you are asking a lot of your body with running - you need to fuel the engine otherwise you will be constantly hungry and that can lead to bad choices and binging.
Let me know if you want to know anything else about MFP.
Edited to say that I see runs with dogs already explained all this - I should read things more carefully.
Edited: 12/11/2012 at 13:21