Okay, so right now there is no way to change your defensive scheme, but here is what you do, and it simulates real football anyway.
1st) Choose the playbook that matches the style of D you want to play. Either choose a coach's playbook like Rex Ryan or Tomlin if you know they run the type of defense you want to run or you can choose the 3-4 4-3 4-6 playbooks. You can choose your playbook when you create your coach and before each game in the Advanced Settings (this is when you see the screen with the two helmets and overall ratings for you to start the game)
2nd) Sign/draft/trade players that match the way you want to play. If you want a player that is good at being a 4-3 Run Stopping Defensive end, then choose 4-3 Run stopper in the Player Position Scheme (More...Strategy...Schemes) and that will show you the OVR for that player when running a 4-3 and you want the type of player that is good at stopping the run.
**Changing position schemes does
not change how a player plays on the field. It only shows you, the human, that player A is better than player B at this type of play. For example TE Jimmy Graham is a 94 when selecting Vertical Threat as the type of TE I want. Because he is a MONSTER at jumping up and making catches and he is FAST. If I choose blocking TE his OVR is only 85.
Because he is not very good at blocking but he is
still a MONSTER at jumping up and making catches and he is
still FAST and will keep making those catches for you. You can just see that he is not very good at blocking, since that is the player scheme you have chosen.
Hope that helps.