Hi,
the answer is simple, but not "logical". It took me a while to figure this one out the first time....
Go to the mixer, and set the automation from the Stereo Out channel strip from "off" to "read" (it's the rectangular button just above the VU meter; see Help > Logic 8 Express User Manual, page 577 for a picture).
Now you should see the Master Track appear in the arrange window, so that you can draw automation (volume fade out) into it.
Regards,
Jaap