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Your water seperator and fuel filter are a combined unit mounted in the center of the engine valley underneath the black plastic cover. Simply turn the yellow tab on the side of the filter housing and it will open a valve that drains the bowl. I would suggest replacing the filter and cleaning out the bowl at the same time. The fuel filter cover is the round black plastic lid on top of the housing and will unscrew. Hope it helps.
If you look on the left side of the fuel filter canister.....as your facing the engine compartment. Along the bottom edge......you'll find a lever. That's how you drain it.
Now for the messy part. If you go under the truck and look up along that same left side along the front edge of the engine.....you will see a 3/8" tube comming down. It isn't long enough to come down where you can catch it in something clear.....so there is no way of seeing: 1.you've got water there. or 2.you've drained enough to remove all of the water....and now have only diesel coming out.
So what most people are doing is getting a piece of 3/8" hose from your local auto parts store. And installing it on the end of that tube. Then run it out to the front of the truck where it can be secured. Then a clear container can be held under it while someone opens the lever. Or....you can just say to hell with it, and just dump some fuel on the ground, and not really know wheather you are getting water with your fuel from the local station or not. The choice is yours on that issue.