Options for configuring CopyTools startup and exit options can be found on the General tab in the Options dialog.
To have the CopyTools start minimized to the system tray:
By default, closing the main application window simply minimizes CopyTools to the system tray and stays running. To change this behaviour and have CopyTools exit when the main window is closed:
By default, CopyTools only runs shutdown profiles when it receives notification of Windows shutting down or restarting. However, you can also have profiles run when CopyTools is exited.