I mounted my flares in place with some of the wide jaw vice-grips, to get them exactly where I wanted them. I then traced the outer edge with a pencil. After removing the flares, I did as Broncosbybart did and measured 1 1/2" below the pencil mark and marked that with a sharpie. I used blue painters tape over the sharpie mark, which was visible through the tape. I used a high speed air cut-off wheel and it cut them off nice and clean. I was concerned about marking and pre-drilling the flares, as screwing up wasn't an option (Expensive). I PMed Jim at WH and he recommended a 1/4 space between top of flare and hole and a 2 1/2" spacing between holes. I used a silver sharpie and marked the flare before drilling. Didn't come out perfect, but that was operator error. Putting them on from there was simply a matter of taking my time and making sure they were lined up where I wanted them before I drilled the screws. Again, I used the wide-jaw vice grips to hold it and checked about five times before each flare was drilled into place. Even had two second opinions for each flare to ensure the backs and fronts were evenly spaced from the body line seam. A critical eye can see the mistakes I made, but if you're looking that closely you have too much time on your hands. Good luck!
