Use two cameras to photograph the same image from two positions to create your images for each eye. Even though your image will be out of focus and jerky, you must achieve some degree of control over the final image.
Work with your images or footage in 3-D glasses to structure your 3-D vision in motion.
Project your images simultaneously from two different angles and use two filters--red and cyan or blue or green. Commercial venues prefer polarized method for 3-D viewing. It means that the light polarized in a perpendicular plane exhibits different retractive sequential arrangements of material.
Study the 1969 experimental film "Tom, Tom, the Piper's Son", by Ken Jacobs. The film consists of retouched footage of a 1905 D.W. Griffith film of the same name, based on a popular nursery rhyme. The 3-D technology of the time made the interactive version of the film possible. Jacobs was able to work with the computer and, using the spectacles, see what worked and what didn't moment to moment. He infused two frames with the figures to make time into depth.