Most skin boat builders coat their frames with a few coats of linseed oil and thinner which travels into the tight spaces easily. Lay your boat on its side and sponge it out when you're done. The frame will never, ever rot on you. It will probably never rot even if you did nothing but keep it dry between paddles.

Chris Cunningham told me the only rot he's ever seen is a canvas skin that rotted around the coaming where water can get trapped. If the skin is synthetic, you don't have that worry, and even that would only occur after many, many years.