Steven Pinker, a philosopher with whose views I generally do not accord, has a good review of a book on self-control. While some neuroscientists have used their work to cast doubt on free will and autonomy, their lessons properly interpreted are showing us new ways of exercising command over the machine.
Immediately after students engage in a task that requires them to control their impulses — resisting cookies while hungry, tracking a boring display while ignoring a comedy video, writing down their thoughts without thinking about a polar bear or suppressing their emotions while watching the scene in "Terms of Endearment" in which a dying Debra Winger says goodbye to her children — they show lapses in a subsequent task that also requires an exercise of willpower, like solving difficult puzzles, squeezing a handgrip, stifling sexual or violent thoughts and keeping their payment for participating in the study rather than immediately blowing it on Doritos. Baumeister tagged the effect “ego depletion,” using Freud’s sense of “ego” as the mental entity that controls the passions.
Baumeister then pushed the muscle metaphor even further by showing that a depleted ego can be invigorated by a sugary pick-me-up (though not an indistinguishable beverage containing diet sweetener). And he showed that self-control, though almost certainly heritable in part, can be toned up by exercising it. He enrolled students in regimens that required them to keep track of their eating, exercise regularly, use a mouse with their weaker hand or (one that really gave them a workout) speak in complete sentences and without swearing. After several weeks, the students were more resistant to ego depletion in the lab and showed greater self-control in their lives.
Now that you know this, you have another toolset for exercising autonomy. Your unconscious mind may be making decisions from moment to moment before the issue rises to your conscious control: but if you set long-term goals, and keep track of adherence to them, you can steer.
If you find yourself having trouble, eat some chocolate, drink some soda, and then get back to it.