I have a 14" Hobie Pro Angler that weighs over 100 pounds. The secret to easy loading is a pair of Hully rollers bolted to the rear crossbar. This picture shows them on my previous vehicle:
When I bought a new vehicle, I ordered aftermarket crossbars from Thule and installed the rollers. The positioning of the bar meant I had to also fabricate a guide/slide pad to protect the rear spoiler as you see here:
I also made up a block that fits inside the Hobie's Mirage drive well, for added stability. Once tied down, the 'yak can't move in any direction thanks to this block, even a freeway speeds.
A different style 'yak would require a different block design, of course.
Here it is, loaded and ready to boogie...
Happy 'yakking!