Feel free to reward yourself from time to time with those extra calories. It is in the end a question of balance. Given a healthy diet and a steady exercise routine, your body will find your natural healthy weight on its own. With a little planning, you can help it happen that much faster. But give yourself time.
Crash diets are a fantastically bad idea.
The best way to lose weight is by dedicating yourself over a long period of time to good eating and exercise habits. You are in the right place. As weight-loss exercises go, running is right up at the top. But high-intensity exercise, like running, burns more total calories, including a higher absolute number of fat calories. That said, this does not mean that you should necessarily do heavy, intense sprinting to burn the most fat.