cineSync supports stereoscopic media rendered as a single file - that is, the left eye and right eye rendered side-by-side into the same Quicktime movie.
Firstly, load the left/right rendered Quicktime into cineSync and select the media for playback.
Then launch the Stereo Settings panel from the View Menu or from the transport control bar. Once you check the 'Enable Stereo' box in the Stereo Settings pane, you'll be able to utilise the various Stereo tools..
When Stereo has been enabled, you can select how view the media, depending on your output requirements.
There are Anaglyphic and Grey Scale viewing options, plus an easy check box for viewing Anamorphic images.
Adjusting the Image or Overlay Convergence will change the apparent depth of either the media image, or of any annotations. This can be very useful, particularly if you are annotating over media that "projects" beyond the screen - you can ensure gthe annotations always sit "in front" of the media so as not to disrupt the viewers' depth perception.