I think what Hairdryer is trying to explain is this.
You play your first game of the day. Afterwards your next game is shown on the home screen. In the information box alongside match preview you will be told how many rests and moral boosters your starting lineup needs to be fully prepared for the following game. You will also be told how many training sessions your team needs.
But your training sessions (usually 2 or 4) can be made up of only 1 player doing 1 drill. So take a reserve striker for example, someone who will definitely not play in the next game and give him a training session of 1 skill drill, condition drop 0.75. Hit repeat if only 2 training sessions needed, again and again for 4. This complies with what the engine wants of you to have your team fully prepared, but how can doing this training have an effect on the whole teams preperation? It shouldn't. It should only affect 1 player.