a) I can't answer about the 3d, I haven't gone that route yet.
b) Since you are using MKV's you are not converting the audio, if you want to decode your HD audio properly at this time you NEED to use an external player (I use Media Player Classic HC) and configure it to bitsteam to your AVR. With the latest XBMC (v11, "Eden") I saw a patch on their forums that enables bitstream out but it is not official and I have not played with it yet either although the feedback looked good.
Just an FYI if you didn't know about that portion of it. Good luck! I too love having all my media at my fingertips and hopefully soon, we won't need to fiddle with external players at all.
An expert at anything was once a beginner...
Founder of the "F-WAF" group.
" WAF?!? F*** WAF! I put in on this house too you know... " =)