My wife is the fisher in the family, using both flies and bait. She prefers Scotty rod holders. On her newer SOF we used a rectangular plastic flush mount. We just bolted it to a plywood plate. On her older stripper we wanted something fancier so I turned a flush mount out of maple. I epoxied it in place. It looks and works the same as their compact threaded mount (#444). For that one just drill a hole through the deck and screw on the mount.
http://www.scotty.com/fishing-gear-equipment/fishing-rod-holders.htm