Conscious control means inhibiting the habitual reaction to a stimulus, and reasoning out an effortless way to conduct any given activity. We take conscious control of ourselves by acquiring the skills of inhibition and directing, which enables us to detect and change our bad habits.
FM Alexander gives this definition (The Universal Constant of Living, p12):
I wish it to be understood that throughout my writings I use the term "conscious control and guidance" to indicate primarily a plane to be reached rather than a method of reaching it.