this video explains the Ford/Bakflip HD cover pretty well:
http://www.youtube.com/watch?v=nEySZ0bLgAI
It locks when it closes. Then you just make sure to lock your tailgate handle (that's where those electric tailgate locks come in handy, I put one on my truck). There's no exposed handles, latches, or keyholes that you have to worry about a theif trying to break into.
It has rubber hinges and rubber seals along the outside edges of the cover (that extend on top of the bed rails and tailgate lip). Water that gets under the seal or hinges is collected by the drain rails.