Is there a way to specify inputs and outputs for structures?
Solution 1:
Not in vanilla, afaik. You've got to work around the set inputs. Hopefully this changes at some point, but for now, there's nothing you can do besides modding the game.
And speaking of modding, I believe this mod will do what you want for inputs at least http://www.factoriomods.com/mods/gdiw-gha-darnitwater