System Prefs shows both drives although I'm not sure which it thinks is the startup drive. If that's determined by placement in the window, the startup drive is on the left.
HINT: When I create a clone or alternate boot drive, the first thing I do is change the desktop picture on the clone.
My system still does that automatically. The Backup drive is always orange with the Firewire symbol and the Time Machine drive is always green with the clock hands surrounded by the counterclockwise arrow.
