Team Training - 1st 3 weeks pre-season a mixture of Fitness and Teamwork, on Very High. Use Ass Man reports as a guide for whether Teamwork needs 1 week or 2. After that, Tactics at High for rest of season, because it's the only training category that works on Concentration.
Match Prep - Tactics Only, with no rest, during pre-season. Then I generally hand it over to my Ass Man and let him deal with it.
Opposition Instructions depends entirely on your opponents for that match. I always make sure I have an Ass Man or a Coach with a Tactical Knowledge of at least 15, then I use their advice pre-match and at half-time.
I rarely use shouts, TBH. Work Ball Into Box and Exploit The Wings are the only ones I generally use, and that depends on whether their centre-backs/full-backs are slower than my forwards/wingers (respectively).
Hope that helps. Any other questions, just let me know