Placement of Reese standard bed rails?

I think I have the same set up you are looking to install. The bracket which use the existing holes in your truck frame determine where the bed rails end up. I assembled them first on the TV frame and then drilled the holes in my box from the bottom up. I drilled very small pilot holes first to make sure everything was proceeding correctly.

Like others have said you should have your hitch assembled in the rails first before drilling to eliminate any minor misalignment in fit.