We did a two week trip and knew I would be locking stuff in the back. I got an ARE cover specifically for this trip. I negotiated this into my purchase after we were done quibbling about the price so I got a great deal.
I know it isn't the most appealing ascetically, and they are heavy, but I felt comfortable leaving stuff locked back there overnight in a hotel parking lot. Sure was nice not to have to worry about weather too.
I will be building a rack for it in my garage for when I am not using it as I don't plan to run it all the time. I will likely keep it on all winter because it is nice to be able to throw crap back there without filling up the back seat. My dad has the same cover for his F350 and has a rack in his garage that hangs from the ceiling and pulls up out of the way. I put in on last time I borrowed the truck and it was pretty simple. Best to have two people to move it though.
That being said, I would likely do some kind of hard, lockable cover again. I have read great things about the backflip but don't have any experience myself. Good luck in your quest and have a great trip.
I also have a black Xcargo car top carrier/roof rack pod that would fit nicely in the bed and strap down in a pinch. Just food for thought.