Originally Posted by JoeWPgh
You want to test fit the neck in the pocket. It it's a bit sloppy in the fit, you'll want to triple/quadruple check that you have the geometry lined up so that the strings, when equally spaced, cross the pickup poles and are reasonably centered on the fingerboard.
Now you'll want a clamp - one of the cheap plastic ones with the rubber protectors from Home Despot will do. Clamp the aligned neck to the body so that at least 2 of the body's screw holes are accessible. Select the right sized drill bit for your screws. Hold the neck screw to your drill bit and spike the bit with some masking tape. This is so you don't drill too far. Drill the accessable holes. Unclamp, and screw though the metal plate and attach the neck. Drill the remaining holes and run those screws.
I would suggest if using this method; instead of drilling the holes while the neck is on the body, mark the hole locations using a center punch. Once all the holes have been marked, unclamp the neck, then drill the holes using a drill press or drill guide. A couple years ago I drilled the holes on my allparts neck while it was clamped to my jazz bass and quickly realized that getting a hand drill centered when you can't see the hole you're drilling is very difficult.