The short edge should definitely be on top else the metal won't lay flat on the leading edge of the rib. Plus neither you or the airstream will see it later. General construction order:
1) pilot drill the hinge. My technique is here:
viewtopic.php?f=34&t=1877Others use the ruler trick.
2) transfer hinge holes into the short edge only. Put the hinge aside.
3) Drill the front of the ribs to the skin. Make sure they are pushed down tight against the skin on your nice flat table. Skip the hole where the hinge goes.
4) drill the rest of the ribs to the skins.
5) take clecoes out of the top skin (ruddervators and ailerons, bottom skin for flaps) so you can lay it on the nice flat table. Using my tape trick transfer the hinge holes to the other half of the front skin.
6) cleco the hinge on, put the clecoes back in the top skin, and updrill everything.
Though there are no CNC holes the control surfaces were fun and easy to do.