ff•works makes it easy to add 3D video metadata for YouTube to recognize it is dealing with 3D video.
It appears one just needs to add to the MKV encode setting:
-x264opts "frame-packing=3" -metadata:s:v:0 stereo_mode=left_right
to the General>Custom Encode options
Side by side squeezed videos can then be uploaded to YouTube videos for processing and presentation in either 2D or anaglyph 3D--or SBS for 3DTVs.
Go to http://www.ffworks.net
I export a Pro-Res file from Final Cut Pro X and then do the final compression via ff-works.
This works with different aspect ratios, although you need to specify aspect ratio if needed. (Experiment)
Here is the preset (the file is zipped):
