What causes the changes in the state of Pokemon in Super Training?

Question

You know, like on the bottom bar, where they're either right side up or on their side.

Answer 1

Occasionally, the player's Pokémon wil ltake a rest from Core Training, indicated by the Pokémon lying on its side with a "…" displayed above it and a refusal to participate in a Super-Training Regimen (or accept a new training bag); tapping the Pokémon will wake it upand give it a second wind (shown as a smiley above the Pokémon), which doubles the speed at which the Pokémon can finish off a training bag. ~ Bulbapedia

A Pokémon will be neutral most of the time. It will fall asleep if you it sits idle for too long, and occasionally in between Training Bags. It will wake up once you tap it, become "refreshed" and defeat the first Training Bag you give in half the time. A Pokémon that is KOd will not wake up if you tap on it and will only wake up once it has been revived.

Sources: Bulbapedia and Personal Experience.

Answer 2

Pokemon that are their side are Pokemon that haven't been used in ST as often as those standing up. Sleeping Pokemon are fainted.

Answer 3

its when a Pokemon is taking a rest from core training. During this time you cant Super Train or you Bags on that Pokemon. Tapping it will wake it up and energize it Making them Clear bagstwice as fast for a few mins.

Source: http://bulbapedia.bulbagarden.net/wiki/Super_Training