So I run 3 times a week for about an hour each time but its more like jog then walk and repeat. So what I want to know is will this reduce the amount of fat burned if I where jogging the entire time?
Well the faster you go the more calories you'll burn, however if you walk uphill for example, you might burn just as many calories as you would jogging on a flat surface. My friend and I both sometimes work out together at the gym. I jog uphill on the treadmill for 45 mins. He runs fast on a flat treadmill for 45 mins. In the end, I sometimes end up burning the same if not more calories then him.
Running, bicycling and walking all consume calories. Fat stores are used when you exercise- it's just a matter of how intense the exercise is. Walking up an incline- like a hill is as intense as running, so it's not as much the exercise as it is how hard you're working and how long you're doing the exercise. Generally 30 minutes is the minimum length of time in order to be effective.
Try doing fartleks. =] Fartlek - Wikipedia, the free encyclopedia It does sound pretty similar to what you're doing though, so I'd say as long as you feel like you got a workout, you're fine.