Sorry for the late reply. Here's how I haul my 12.5 foot kayak in my Tacoma. This is a Wilderness Systems sit-inside. I wrap that ratchet strap around the cockpit gunwale and through the rear corner truck bed "D" rings.
For my Hobie, I run the ratchet strap either through the carry handles or the drive well. I run a "python" type cable lock through there also in case I stop somewhere for coffee and a bagel on the way home.
Sometimes I use a $100 (Etrailer) folding bed extender.
Either way, the truck bed cover is not needed but it does help keep the nose of the kayak in the corner of the bed.
Hope the photo below helps.
