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.
Some models, like the Pentax K-01, allow you to change the size of the live view AF area. On Olympus models, if you magnify the live view screen while focusing, the AF area stays the same in the viewfinder, but since the image is magnified that same area is more precise. (See Olympus's FAQ.) Even on cameras where the AF area size doesn't change when the viewfinder is magnified, this can be helpful in making sure you're getting the intended focus.