With the yak on the ground straddle the back of the cockpit. Put the back of the cover, with the knot, onto the combing. Find the "pointy" end of the cover and streach it foward to the front of the cockpit. Hook it on the front of the combing. Run your fingers along the side putting the bungee under the edge of the coming working foward.  Back side always first then move foward. The best ones have a snap hook foward to connect to deck lines and a strap mid cockpit to insure it doesn't "womp womp womp" down the highway.

   http://www.youtube.com/watch?v=Kcly5HMYVmA

The interesting thing is that if you leave the cover off it gets more rain in when stopped than when moving.

Yes to Grumpy's post. That's how you put it on. However, I had the same maddening problem as you with my WD12 cover until I loosened the knot on the bungee cord.  That extra little bit of length made all the difference.    

   Just remember you don't want it loose.

You can adjust the knot. However if it goes on with great difficulty put the cover on and place the boat in the sun. Leave cover there for hours. Let it get good and warm. It will set to the right size.