To use the two region auto focus the regions must be defined prior to running the auto focus.
Click the 
button, and click on the live preview image to position the bottom-level region.
Click one time more to lock the position.
Do the same for the top-level region.
Then the region can be sized.
When region is defined just click the 
button to run the two region auto focus.
After the focusing, bottom- and top-level values are transferred to the Focus Automation panel - then extended focus or topography/3D can be run with ease.
After two zone auto focus. The regions show the z-level values.
Note: If zones are defined, you can also simply click extended focus or topography buttons directly.