I use a scotty's fly rod holder on the left side midships and usually have the rod at a 45 forward and up and paddle under it. The rod won't break if a fish hits. I just paddle-trolled 5 nice trout this way in a lake. The trick is to get the rod holder forward enough to be able to paddle under it and yet be able to reach the rod and extract it in a smooth motion.

I'm talkin' SOT kayak....,but maybe it applies a little..