So, I'm going through the elite 4 and champion with the exp share turned on to level up under levelled Pokemon, do they still get evs or do they only level up?
If a Pokémon holds an Exp. Share, it will receive effort points even if the battling Pokémon has maxed out its effort points. If the Pokémon with the Exp. Share has Pokérus, the amount of effort points received is doubled. Source: http://bulbapedia.bulbagarden.net/wiki/Effort_values#Generation_VI