As yet, it's REALLY fiddly, and I haven't really found a proper solution. I can run the Blu-Ray disk through MKV and then through HB if a preset is required, but in MKV you can merge the output files ( usually get around 10 on a 3D 2 hour movie) But you have to merge them all...even 1 second files are important from what I've found...It's all about overlays and It's pretty new so things should improve. Take a look at this thread for a workflow idea:
I'm still experimenting, but as the thread got no replies I kind of figure everybody is in the same boat. To be honest the 3D aspect of it is not that big a deal...I have the originals and only really need to rip them for use on my ATV's and iPad.....It's just interesting to see what can be done..I'm not planning on burning many copies or anything....I did do a couple and they came out fine...But in 2D!