I tap the neck with a rubber mallet gently to make sure it's completely seated.
Then I clamp the neck and body together with an Irwin Quick-Grip bar clamp. These have rubber faces that don't leave traces.
I then use a Transfer Punch to transfer the body hole centers into the back of the neck.
Using these punch marks, I know my pilot holes will be perfectly centered when I drill them on my drill press.
If I'm using brass inserts in the neck, I drill the larger insert holes, then install the inserts with white glue.
If you don't have a Transfer Punch Set yet, it's the best $8 you will ever spend:
http://www.harborfreight.com/28-piece-transfer-punch-set-3577.html