Every player gains 6% of their condition every 3 hours. This can be seen in training->physio center.

Every legal formation works against something I guess. Maybe it's more of that your tactics support your formations. For example, if you attack down both flanks, I think it's better to have some wingers too (or wide midfielders). Overall I don't think formations are that important if your team is otherwise in good condition.

Train your players every morning to keep your bonuses full. 2 easiest trainings from every category (att, def, phy). It will make 6,75% per training session and you need 2 of those, if you watch the ads. If not, you need 4. If you watch the ads wisely, you don't need rests so often.

The number 1 in your training tab probably means that there is something that the game wants to show you. Just guessing here.