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 may allow you to change the size of the live view AF point. 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.