Easiest way is choose a formation you're happy with at the start of the season then make sure your 11 reserves duplicate the positions in your XI. Job done.
Obviously if you can pick out players that can play multiple positions, then that will be a bigger advantage, especially if you're like me and your whole midfield is out injured.
This strategy is based upon me not wanting to tamper with my formation very often due to nordeus's primitive game engine. That's why i've gone with a solid 4-4-1-1 and stuck with it regardless of opposition squad rating and level.