Tray icon provides quick access to some application functionality and is used to notify you about significant changes during application execution when the main application window is minimized or hidden with other windows. To configure application behavior regarding the system tray click Preferences button from Application Menu and switch to System Tray preference page using the appropriate link in the navigation bar on the left of the Preferences dialog.
If you prefer the application main window to be minimized when the application is started you should check Minimize on start up option.
Show application icon in System Tray option allows you to choose if the tray icon and all its functionality description above should be used with the application. If this is enabled you can also specify if the application should be hidden from task bar when it is minimized to tray and if the main window is restored from tray with single or double click.