The way I do it is to clamp the neck to the body, and make sure it's straight... some neck pockets can be wobbly.
Then get the proper size drill bit for the neck screws. The bit diameter should be smaller than the threads, and slightly larger than the shank.
Figure out how deep the drill will have to go into the neck, and either use a drill stop or a piece of tape on the bit to mark the maximum depth. You don't want to drill all the way through the neck! I did that once...
Then using the body holes as guides, drill your holes into the neck heel stopping at the tape.
This is similar to the above, but uses less steps, doesn't require duplicating punches (always good to have! We have two complete sets) and the body holes will maintain the alignment of the new holes you are drilling.
This also works well for using threaded brass inserts and machine bolts, which is what I do.
There are many paths to the same destination.
