If a run short is realised before the ball is scored, click the End Over/Umpire Signal button, select Run Short from the menu, then score the number of legitimate runs, as usual. These runs will be awarded, and the Striker/Non-Striker will be automatically adjusted to allow for the Run Short, and the number of legitimate runs will be underlined in the Play Control -> This Over section and in the Ball by Ball panel:
If a run short is not realised before the ball is scored, either use Undo Ball/Over/Action to delete the ball and re-score it as above, or click Edit, select End Over/Umpire Signal -> Run Short again, change the runs awarded to the legitimate number, and click Edit to commit the update. As above, this will automatically update the Striker/Non-Striker, Play Control -> This Over, and Ball by Ball details accordingly.
If a run short is realised before the ball is scored but Run Short is not included with that scoring, e.g. the batsmen run 2 with a run short but 1 is scored, which is not then re-scored or edited (meaning the legitimate number of runs is correct but the wrong batsman is on strike for the next ball), it can be added by clicking the Swap Batsman button next to the Striker dropdown (or selecting the Non-Striker from this dropdown)
On the Auto-Correct prompt, then select Yes – Run Short. This will swap the Striker/Non-Striker batsmen and add the underline to This Over and Ball by Ball as above.
The Run Short can also be removed by either clicking Swap Batsmen again or re-selecting the original Striker from the dropdown and on the Auto-Correct prompt selecting Yes:
A Run Short can be added to or removed from a previous ball (i.e., not the last ball scored) by clicking Edit, highlighting it in Ball by Ball, and ticking (to add) or unticking (to remove) End Over/Umpire Signal -> Run Short. In both scenarios an Auto-Correct prompt will appear with the required changes to all subsequent balls, so click Auto-Correct to accept these changes and Edit to return to normal scoring.
NB: If two short runs occur, simply score the legitimate number of runs as usual, as this has no effect on the Striker/Non-Striker, so for example score a 3 as a 1 and a 2 as a 0.
Please also watch the following video on the Short Runs function: