Fat loss is just math. 3500 calories = a pound of fat. So if you take out 250 calories a day from your diet and burn 250 calories a day on a run or stepper or whatever, you will loose 1 pound of fat a week (250 + 250 * 7 = 3500).

If I was dedicated and wanted to loose fat, but retain as much muscle as possible, I would run in the mornings hard and fast for 30 minutes, 3 times a week and workout at the gym 4 times a week.

If you want to run and workout on the same day, I would say run in the morning and workout at night.