I can't comment on whether or not it is better to extend past the tailgate or not. To do a partial tonneau cover, I believe it is best to separate the covered and uncovered parts of the bed. Basically have a vertical wall at the front edge of the partial tonneau cover, from the bed floor to the height of the cover.
This is what Gale Banks did on his top speed record setting Dakota.
Sidewinder Dakota:
http://www.google.ca/imgres?q=sidewi...9&tx=133&ty=70