During pre-season, have the schedule fairly high on strength/aerobic/tactics, and fairly low on everything else. Then when the season starts change it up to a lighter schedule.
Get top physios in, such as Gary Lewin, and top fitness coaches, such as Paul Winsper(both free agents). The other thing is to be religious about rest. I always give my player 1-2 days off after a game, depending on schedule, and as the season progress I will give them up to 3 days off if needed. Toward the end of the season, I will give them 4-7 days off if necessary! I barely get any injuries.