Player instructions VS Player preference?

What I've realised is that there are a lot of player instructions a manager can give to a player and I feel like I'm literally controlling players like a puppet with strings attached.

Obviously the player has his own stats and know their own strengths and weaknesses and should play into their own common sense?

My question is, How much does it balance out, do players literally follow all my instructions or a mixture and play to their strengths and follow most of my instructions?

As a long-time lower league manager, I can tell you from frustrating, painful experience that players rarely follow literally all of your instructions. You can tweak both team and individual settings such as creative freedom and roaming to force better adherence but you'll never tie them down like puppets. At least not my free spirits. The degree to which a given player follows instructions is not driven so much by them playing to their strengths as by other "attitudinal" factors such as work rate, concentration and decisionmaking.

Like AytchMan said, it depends a lot on mental attributes. For example, you can set a player's instruction to often though ball and often cross ball, but if his teamwork attribute is too low, he won't pass.

PPMs also play a big role in dictating what players do.