I have a Chesapeake 17. I transport it in the upright position. This seems to work well. I pick the boat up by grabbing the rim of the cockpit, then I hoist it onto my right hand/shoulder. The left hand stays on the rim to balance and aim the boat in the wind. From this position, it makes sense to just slip the boat upright boat onto the racks.

I built wooden cradles to fit on the Yakima racks on my van. I took a contour gauge to the bottom of the boat at two points the same distance apart as the racks on the van. Transferring this contour to the cradles gives you "custom made" surfaces on the cradles which match the bottom of the boat almost perfectly. This spreads out the load much better than resting the boat on a surface that doesn't match.

I built fairly wide top surfaces on the cradles - about 4" - and covered them with strips of an old foam sleeping pad - contact cemented into place. The foam spreads out the load even more, since my "custom-fitted" cradles aren't perfect.

I use cam-lock straps from NRS to secure the boat to the racks. I always use front and back lines to secure the boat to the car. We had some people post on our local club's listserve about incidents where the cam-locks on their straps failed. It seems like it would be a pretty rare occurence, but it isn't too tough to attach the ropes, so I do it. Not only do I not want to lose my boat by having it fly off my van at freeway speeds; I also shudder to think of the damage it could do to something/somebody it hit. I think that, if the cam-lock straps did fail and the boat was only held on by the front and back lines, it would bounce around up there, and that would be a problem, but I'm hoping there would be enough tension to keep the boat on top of the van until I could stop, pull over, and fix things.

Lastly, I have a cockpit cover I can put on in case of rain. It didn't cost much. Most places that sell spray skirts have them.