The wagon wheel can be fully rotated 360 degrees to suit your needs/scoring position by moving the bar at the bottom left or right:

When an over is completed the bowling end will automatically change.

Clicking on the  icon in the top right hand corner of the wagon wheel window will allow you to 

Please Note: Off and Leg side will automatically change if the batsman is left handed.

Scoring:

To note where runs have been scored simply left click on area the ball has gone. A yellow line will appear showing the trajectory of the shot.

If you would like to change the shot placement on the wagon wheel, left click on the correct area. To remove the shot completely right click once anywhere on the wagon wheel.