Here's my take on mounting a rod holder for trollling, etc. Any other views? I use a Tite-Lok holder.
To waterproof the mounting holes, I use 3M 5200 sealant ($10 or so a tube at your favorite marine supplier) when I mount a new holder. I always add a large backing plate under the bolts, beneath the deck, and use washers also, to spread the load.
I think (though there are many, many opinions, some vehement) that the best place to mount a rod holder is just forward of your ****pit: just far enough forward that you can grab the rod out of the holder in a hurry, but not so close to your body that it interferes with your paddle stroke.
You can troll this way, and thus watch the rod tip for hits; also, the rod is always there at the ready for spincasting to a breaking school of stripers, blues, or bonito, of which on the Cape and elsewhere, where I fish, I am lucky enough to find many.
The Tite-Lok is not a permanent holder, just its base is. Which means I can take the holder off when I just feel like paddling.