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Synchronization
The cameras should be synchronized so that they take pictures at exactly the same instant. Otherwise, when you do the tracking and solving, you will by definition have some very subtle geometric distortions and errors: basically you can’t triangulate because the subject is at two different locations, corresponding to each different time.
To make life interesting, if the film will be projected using a frame-sequential projector (or LCD glasses), then the two cameras should be synchronized but 180 degrees out of phase. But that will mean you can not track exactly, it is the worst possible synchronization error. Instead, for provable accuracy you should film and track at twice the final rate (eg 48 or 60 fps progressive), then have the projectors show only every other frame from each final image stream.
If circumstances warrant that you shoot unsynchronized or anti-synchronized footage, you must be aware that you (and the audience) will be subject to motion- related problems.
CMOS cameras are also subject to the Rolling Shutter problem, which affects monocular projects as well as stereoscopic ones. The rolling shutter problem will also result in geometric errors, depending on the amount of motion in the imagery. To cover a common misconception, this problem is not reduced by a short shutter time. If at all possible, use synchronized CCD or film cameras. Note that when CMOS cameras are used in common mirror-based stereo rigs, the rolling shutter effect will go in the opposite direction (bottom to top) for the mirrored image: if you have to mirror the image vertically, you have to correct the rolling shutter with a negative values as well.
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