I think the entire new training system turns on the bonus. When I win (and I mostly win after the update), my ass man never neglects to mention that the training and bonus helped. Sometimes, he devotes two comments to the same idea.
Of course I have to train for maximum bonuses!
Step 1. Pick players that will ensure a bonus. I.e, at least 4 attackers, or 4 D, or 4 midfielders, 8 in total if possible.
Step 2. For the players picked, pick the right sets.
Did you notice how these options are located on the screen? First (on the left) player selection. Second (on the right) drill selection. That's the order you should chose. Unless you are Arabic, of course, in which case it is all wrong.
A little rest at max condition is a complete waste. I noticed that you apply a lot of "common sense" and "real life" concepts to how you view and play the game. While that may be fun for you and make you a fascinating player to watch and learn from, it also has little relation to the reality of the game (by "the game" I mean T11, not soccer). You just have to learn to think like the program. Or rather, the people who wrote it. I meant, you don't have, to I do.