After having created a video output for your left eye and one for your right eye with VideoStitch Studio, you can use ffmpeg to combine them.
You can use the following ffmpeg commands to merge your 2 video outputs :
Top/bottom:
ffmpeg -i left.mp4 -vf "[in] pad=iw:2*ih [left]; movie=right.mp4 [right];[left][right] overlay=0:main_h/2 [out]" output.mp4
Side by Side:
ffmpeg -i left.mp4 -vf "[in] pad=2*iw:ih [left]; movie=right.mp4 [right];[left][right] overlay=main_w/2:0 [out]" output.mp4
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