One often overlooked entry point is the output jack hole. If you have, to, on a Les Paul styled instrument you can go clear from the output jack hole all the way up to the 3 way switch if you're careful. You can't have a "walking" drill bit or else you'll come out somewhere unexpected! I've done it all different ways. Some channels under figured tops, some holes drilled from wacky angles, and some just plain crazy ideas like routing the side of the bridge humbucker with a dovetail bit to make an angled entry that protrudes into the electronics cavity and makes a nice open rectangle. I like to make starter holes with the dremel and a round cutter when I'm entering at an angle. Often times I'll wrap tape around my fingers and thumb so I can grab hold of the shaft part of a longer drill bit to guide it while it's spinning. Is that enough information?
Really every hole "could" be done with a long drill bit, even the Les Paul. You could drill the pickup wire holes from the tenon joint before you attatched the neck, do the 3-way from the output jack, and the bridge stud from the electronics cavity. Even if the neck was already on you could still come from the output jack to both the neck and bridge pickups.
I agree with toshiro but would add that the newer RG's are still drilled from the neck pocket, but there's no back to many AANJ's so the first point of entry is the neck pickup wall. Those are awesome because you have enough angle to drill each pickup to the electronics cavity directly. That helps sort the wires in there.