If I had to fish the waters around SD all year round where the surf gets a lot bigger than it normally is here in SB, I would probably do the following:
Separate rods and reels. Store reels in zip-loc baggies (or dry bag) inside a hatch. Lash rods together with a strip or two of velcro and attach them to the side of the yak using the paddle keeper, but also put a bungee-based tether on them just in case.
99.9% of the time up here, I just launch and land with them in the rod holders on my Crate mate. The worst thing that happens is my reels get washed with sand on the exit, and I have to take 'em apart and clean em out. (thus my Shimano Tekota is missing that *#$&^ little spring-loaded pin that keeps the drag lever tight.... ) ;-)
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