As you run, you focus on your breathing, or on your body motions, or on the environment around you - whatever makes you feel "present", experiencing the moment around you instead of being in your head. And you just keep running without thinking for some period of time.
Couple more bonuses of meditating while you're exercising:
- You can focus on motions instead of breathing. That way you move better, and it's more fun, and it makes meditation easier.
- You don't need a timer, you can just meditate while running a certain distance. Since you're doing it every day the timing will be pretty much the same, and you aren't subconsciously wondering when the timer is going to stop, you can just focus on enjoying your jogging.
If you also practice something like loving-kindness (it sounds hippy, but it has scientific backing[1]), it can increase the quality of your relationships.
[1]http://www.emmaseppala.com/18-science-based-reasons-try-lovi...
It's also much easier to stop the thoughts, focus on the present moment, breathing, etc when you are running in a park as opposed to staring at the wall.