It doesn't matter when you use them, so long as you do. But you want to Super Train them in the values you want before they accumulate EVs from regular battles, for instance before I trained the Vulpix I'm using now, I just sat down and Super Trained it for about two hours in one sitting before I started getting it experience. Even if your Pokemon don't battle, they can still gain EVs and mess up their values, so you want to have them filled out before anything else or it disrupts them. Team: Amaterasu(Ninetales) Houndoom Flareon Delphox Arcanine Rapidash