I set the chosen input port on the AVR to DIGITAL which gives me the tosslink connection with the digital audio from the ATV2 going into the AVR for processing to the speakers. I run the HDMI out cable of the ATV2 directly up to the Flat screen monitor HDMI input of my choice, I have 4 available.
Since I did this instead of using the HDMI cable for AUD and VID into the AVR, my overall sound and I think picture is better. Being somewhat of an earlier AVR, it has 4 HDMI inputs and 3 tosslink inputs, but dont think it was really up to being used that way. MUCH better since I split the ATV2 outputs and ran them directly as described above.