What audio streams should I be including in the mkv?
How does MC select the appropriate audio track, does it need to see a stereo track to output stereo on my system? will it work if I have only included say DTS MA?
I only rip/include the Lossless Audio on all my rips to MKV. MC can/will handle these audio tracks, and only use the best your downstream can accept. This lets you keep only the best audio available, but use whatever you're currently able to process.
The only possible caveat to this is DTS-MA, which Matt pointed out earlier. It's an easy workaround.
If you're not sure your system can/will handle DTS-MA, you can add the core DTS audio for those movies.
Later, if you decide you no longer wan the DTS core audio, you can remove it, without re-ripping the whole movie again. Installing mkvtoolnix gives you an interface called mkvmerge GUI, which will allow you to 'open' the mkv and see all the individual tracks; video, audio, subtitles, chapters, etc, and you can always uncheck the DTS track, and remux, which will just rewrite the mkv without the DTS track, with no encoding, so it's still lossless.