How is it secured to the case? I'd say to drill it without the case present, simply for easier maneuverability, but I understand how that could be an unappealing option, depending on the securing means. Just be sure there is direct support under the area being drilled, like a section or two of a two-by-four. Use a sharp bit, and go easy on it. If you have some extra window material, practice on that first to work on a technique.