I did this and can thank others that have done the same thing that shared their experiences. 

How far apart are your Thule racks?  The best would be to put one on the cab and one on the back of the bed.   And, are they at least 54" wide? (that's the width of the dory)

I opted to use a "T-Bar" approach and had one custom welded for the front of my Honda Element because my Element roof racks arent far enough apart to carry the entire load.  The top "T" part swivels in the vertical tube so the process is, put the dory on the ground 90 degrees to the T bar. Two people pick it up and lay the bow on the "T" then tie down as shown with stern still on the ground.  Then 2 tall people pick up the aft end and swivel it around up onto the rack which can be tricky.   I carry a Trailex 250 trailer disassembled inside the Honda Element, then when we get where we're going to be for a few months, I use the trailer because putting the dory on the top of the car is not an easy feat.  Roof racking your dory as the only method to transport it is not nearly as convienent as using a trailer.  One thought..could you store the boat on the trailer in whatever place you would store just the boat?

You can see the rack I built out of 2x6's here:

https://picasaweb.google.com/lh/photo/kasFEkPyEgMXD0WcqACuzjFolq1y-t7pqfyiNmzJPv8?feat=directlink  Then scroll to picture number 554.

If you are considering rolling it up over the back of the truck there are a lot of You Tube videos on all sorts of methods.  Also, if you want some "wings" to set the rails in, look at Malone Sea Wings..very good quality.  Oh and if you havent built the dory yet, dont use risers on the oar locks...you dont need them plus they can get in the way of any rolling method.  Feel free to call if you like...830 997 8120

Curt

Right side up or down?  I suggest down since you won't want any water to accumulate.  Also be sensitive to the weight of the load and the capacity of the rack. Some are limited to 300#. The boat may be light but added water, snow, dynamic loades, equipment, etc might up the actual weight. 

You might consider the wind and cross wind performance of the truck with the dory up high. It can be done, but are you sure you want to?

Also my observation about truck racks is that the rack seems higher and the boat seems a lot heavier after a 15 mile paddle than it did before the paddle.