It's rather easy once you think it thru. What you need is two different video formats: one for the signal for the left eye and one for the signal for the right eye. What is the difference between them? The source they use, and more specifically, the OpenGL buffer they read from. If you look at the Video Format Compiler documentation, you'll note there's a parameter named eye which can take a value of left or right. You just need to create two video formats, identical in all respects except for this one parameter.
Once you have the two video formats, you just need to create a video combination for them. Let's say you have a managed area of 1000*750 pixels and two projectors. You create two video formats called 1000x750_60l.vfo and 1000x750_60r.vfo. You assign 1000x750_60l to channel 0 at +0+0 and 1000x750_60r to channel 1 at +0+0, too. This configuration differs from split screen stereo that that detail: the channels are not vertically stacked one on top of the other, but they overlap.
And that's it.
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