I've actually stored my 14.5' kayak inside my C a couple times when I've gone solo. Put it in and out through the back window over the bed. Just make sure it doesn't fall over and block the bathroom door when you're inside. Don't ask me how I know.
Most of the time the kayaks or our canoe go on the racks on top of our 14' trailer. Inside are our Harleys (which we prefer over our car as a toad), our mountain bikes, and other extra gear we want to take.
The trailer solves a lot of storage issues for us on an extended trips.