To score Non-Regulation Runs press the blue extras box next to the match settings (cog) icon at the bottom of the page. This will take you to the extras page.
The runs section allows you to score non-regulation runs such as fours or sixes scored by running, or overthrows resulting in a 5. You are able to scroll through the amount of runs by swiping from left to right. You can mark upto 20 runs.
Click on the runs you wish to add.
That's it. You're done.