It's the whole area in the square. Live view uses something called "contrast detection auto-focus", and that works by moving the lens back and forth until the sampled area exhibits the most contrast. Since blur is by definition low-contrast, this is very effective at finding the correct focus.
But, in order to work, it needs an area, first because there's no such thing as contrast of a single point (because, contrast to what?), and second because sampling a larger area is less error-prone.