Gary, I use these things ALL the time, and on many pen boxes. I drill the holes about 1/4” in from the edge. When I bevel the edge I go just a “hair” past the center of the hole from the outside edge. Seat the hinge so the hinge pin is even with the wood and only the round part is showing. And make sure the hinge is perpendicular to the box edge. Let the epoxy dry before you attach the top. Since nothing is perfect in this world, I always make the pen boxes a little larger. After the glue sets up I true everything up as one unit.
I also find that it is more comfortable to take the pens out of the box if the pen slots are 3/4” from the hinge edge of the box. Good luck ….....
-- Odie, Confucius say, "He who laughs at one's self is BUTT of joke".