Many BD players have really dreadful setup menus. Panasonic may not be the worst, but they're not the best, either. (OPPO probably deserves that honor, as they have clearly-defined and separate HDMI audio and digital audio outputs.) There are two settings involved for audio, and ideally they should be separate. That may or may not be the case.

First, there is HDMI audio output. This output supports the different modes you mention (DTS-HD Master Audio, Dolby TrueHD, Dolby Digital Plus, DTS-HD High Resolution) as well as multichannel PCM. The internal decoders offered by this player allow it to decode those formats to multichannel PCM and output via HDMI. If you enable secondary audio, you are asking the player to mix two audio streams - the primary one and the possible secondary one. Many players can't decode the lossless formats and mix two streams, so they pull out the lossy core track (Dolby Digital or DTS) and use that instead. If the player can decode lossless and mix a secondary stream, however, setting the HDMI output to bitstream would force it to then re-encode, and that will always happen with a lossy bitstream. If you start using HDMI audio output, I'd recommend leaving secondary audio set to "off" unless you really need it for something. When setting secondary audio to "on", you should probably also set HDMI output to PCM so you don't ask it to re-encode (assuming the player even allows the combination of secondary audio and bitstream output). The only time I can recall that I've needed to have it on was when I was going through the bonus features on The Pacific mini-series discs.

Second, there is optical and/or coaxial digital output. This can only support Dolby Digital, DTS, or stereo PCM. In this case, you don't really care about the lossless decoders. This is the output you are using, so it's the one you care about. You want to get the lossy core tracks (the highest resolution format you can use with optical and coaxial outputs without manipulation). If in doubt, I'd suggest picking bitstream everywhere it is available. The Model 990 will recognize Dolby Digital or DTS and behave appropriately.