Our trips to Havasu are like four or five hours altogether, and I'm not running a Duramax or V-10 in the Sequoia. I think the truck does better when the boat's covered because of better aerodynamics, but in the end it might give me one extra mpg, no biggy.
When we roll like that, I usually run a strap across the top of the cover between the very aft part of the tower base. This keeps the cockpit area of the cover from ballooning. At times, I'll also run a long strap from bow eye, across the center part of the winshield and back to the ski pole stub dealio UNDER the cover plus the sideways strap OVER the cover. Always cinch down all the straps.
I like the cover, but it's getting a little long in tooth.