The BD30 doesn't have any onboard decoding of the new audio formats (DD+, TrueHD, or DTS-HD). For PCM tracks, you'll want to use the 7.1 Direct input - in which case, the Panasonic's digital output settings are irrelevent, although the speaker settings (stuck under "TV/Device Settings" for some reason) are going to be important. You'll want to set all speakers to large, the sub to on, and leave all of the channel trim and distance settings zero'ed (the 990 will take care of all of that for you). And when using the 7.1 Direct input, you will not see any processing modes engaged on the 990 because none are applicable - it is just managing the multichannel analog signal that is has been given.

The scheme I just described would work for any case you might encounter (except for TrueHD and DTS-HD tracks, which the BD30 can only handle by outputting a bitstream over HDMI v1.3, something we 990 owners can't do anything with). If you wanted to get a bit more complex, however, there are a number of cases where there is an alternate approach available. For discs without a PCM track, the only tracks that you have access to are legacy or core DD and DTS tracks, no matter how you have the player set up. You can use either the BD30's internal decoder or the 990's decoder. Perhaps ironically, using the 990's decoder provides the cleaner and simpler overall signal path. If you want to do a comparison, you could hook an optical or coaxial cable from the BD30 to the 990 and assign that to a spare input, then use that input for any Dolby Digital tracks you encounter. I'd also set all of the digital audio outputs to bitstream and disable secondary audio - otherwise, the internal decoder will be used and the digital output will be downmixed PCM stereo. At this point, toggling between the spare input and the 7.1 Direct input would serve to compare the BD30's decoder with the 990's decoder.

By the way, I've recently picked up a BD30 myself and have spent just a little time with it. In my case, however, the 7.1 Direct input is already occupied by two formats for which I have more software, so I'm connecting it via optical only.