Okay, so I figured out the problem: my 10 month old daughter. She loves to go up to the receiver and open the hidden door and if we don't catch her in time start randomly pushing buttons. It seems that she was able to turn off zone 2 (she must of pushed several buttons to go deep into the settings menu to do this) and so nothing was working in zone 2. I didn't think that there was a problem with zone 2 not being turned on since the day before I used it throughout the day. I guess that I am happy that she is so young and interested in home theater gear. It is good to start them off young.
Anyways, having the stereo audio outputs of the Oppo connected to the cd input of the Onkyo, via rca cables, is the right way to do it. I just had to change a setting in the Oppo player so that it is outputting stereo and not multichannel from the SACD and I am now able to get the high resolution audio in zone 2.
