In the preferences window you can, obviously, set your preferences. The preferences that you can set are:

Enables or disables the use of the of built-in scoreboard.
Allows you to set how entered times have to be handled. At several places in the application you need to enter the time something happened. E.g. a goal has been scored. If your clock counts Up, nothing will hapen. If it counts Down the time will be converted to the time it would be if the clock counted up.
If the general font is to small for you, you can change it with this section. There are 4 options: Small, Normal, Big and Huge.
Click on the "Ok" button to save the new preferences.