Lots of people looking for options on transporting their Hobies - thought I'd share mine.
I like transporting our Outback and Sport upright, and find that the Malone sea-wing carriers conform to the Hobie hull shape well, and mount on the Thule cross-bars well. I like the Thule XSporter racks, because I can lower both front and rear racks below the cab level, to reduce wind noise when their not being used.
I've mounted a 'U-Bolt' to the front sea-wing, to which I've added some 24" rubber trucker bungees, and slipped on two short pieces of rubber hose as cushions. The hose-covered U-bolt fits in the empty Mirage Drive well (with the hose sleeves preventing rub damage), and the rubber bungees easily stretch and attach to the truck rack hold-downs, with their S-hooks, providing a snug fit. Across the rear seawing, I've just used a single bungee. For highway travel, I double up the system with rope as a safety measure - but I've never had a rubber bungee break or release yet. I just replace them when they begin to crack from exposure. Secured through the Mirage-drive well, I find I don't need a bow-line to the front of the truck.
It's a clean, quick tie-down method. It's a bit of a grunt getting the kayaks bow up on the rack's rear cross-bar to start the loading process, but it's doable - even for an old f@rt like me. When the arthritis is acting up and it's particularly daunting, I just lower the rear Thule XSporter bar to its lowest setting, lift the kayak bow onto it, slide the kayak on and over 'centre' of the front sea-wing (resting lightly on the front cab of the truck), lift the rear Thule bar to it's full height setting, and pull the kayak back to its travel position - with the U-bolt in the mirage-drive well.
Hope it makes sense!