Just finished my first detail with the flex over the weekend. As long as you keep the pad flat and keep some motion you'll be fine. The main culprit for burning through clearcoat is heat. The oscillating motion of the flex combined with keeping the pad flat prevents any significant heat buildup on the car surface. If all else fails, you can simply feel the pad with your hand. If its more than "warm" to the touch, then your technique needs changing.
If there are any "problem spots/scratches" that you want to give a little more attention, do at least a 1 foot area around the spot. This keeps heat from building up in a single spot.