The one thing i always say to folk regarding fitness is NEVER start counting callories.

Running will take weight off your stomach, doing cardiovascular related fitness is was you need to do. low reps, longer duration, less breaks inbetween sets.

You need to work for a min of 20mins to get into your 'training zone' or youl be working backwards with no effect.

Coupled with static excercises and raised sit-ups you will tone the area around your stomach helping greatly.