My dad has it down to an art and does it perfectly. We'll mount the bodywork completely (drill everything else) except for the sliders. Obviously the sliders are taken off the bike. Then he'll take a small pencil and insert it where the frame slider goes, so that it's pointing at the bodywork. He'll mark the inside of the bodywork with this pencil as the center of the slider.
Then he'll drill a small hole in the bodywork as a starting point. He then has a selection of round, circular saw-holes (horribly incorrect term there) and uses the one that matches the size of the slider. He then uses the same drill with the the circular "piece", drilling through the center point he started.
Mounting bodywork is a time consuming process if done right. It's even time consuming if done wrong. :) But it's a nice site when the bodywork mounts perfectly right around the frame sliders. :)
edit: he then uses a small dremmel tool to round off any edges and rough surfaces after the main cut. More of a cleaning up tool.