You can also use a straight edge to make sure your work is conforming to the plane of the body. Take your time, and constantly run your had over the affected area checking height. Bondo will work down very quickly. If you have large affected areas, consider getting a DA (dual-action) sander. Again, frequently check the work for proper plane. Once you think you have it work the surface with 180 grit. Spot in the area with a good surfacer-primer spraying past the work. After it dries ck for any pin holes or fine inperfections and fill with spot putty. Wet sand the entire area with 320 or 400 grit. tack off the area and paint
There are other pro grade fillers that are much easier to sand than Bondo. Also, as mentioned earlier use Dynaglass or resin/fiberglass based filler if max adhesion is required or working in a high vibration area