I think we are so far away from this being a concern in fact my top concern is with the age of the guys we are getting back we are going to burn through their service time before we are able to draft enough talent to get to the ML.
It probably will not matter much for the majority of these guys' service time if we use them to their full potential, but if I were constructing a roster, the simplest way to generate extra WAR would be to have a full-time, reliable all-around catcher and a catcher with a less reliable defense who can play 1B/DH and 60 odd or so games at catcher. Consider the Blue Jays and the extra production they were able to get from their two catchers. The average backup catcher is a major negative, hitting at a level that is nearly equal to a pitcher.