Took this idea from a guy on an F150 forums and modified it a little to work on my F250.
Bought four 1/2" 90 degree fittings (sprinkler section at home depot), cut up the existing drain hose and ran the Bakflip drains out the stake pockets. For some of you who don't know, there are factory holes cut from the stake pocket into the bed, I had to drill through my bed liner to access these holes.
I cut down the 90 that is attached to Bakflip drain to try and level out the flow. Used some RTV because it was the closest thing I had laying around as some extra grip for the hose on the Bakflip drain (when I had the full length hose on it would pop off sometimes). Due to their being a defect on my cover I'm supposedly getting a new one shipped soon so I'll use silicon or black RTV on the new one.
View from top of bed rail (stake pocket cover was reinstalled)