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Automatic/Indirectly Solving Mode
The stereo mode effectively uses the inter-ocular distance as the baseline for triangulating to initially find the tracking points. If the camera is moving, a larger portion of the motion can be used to get solving started, producing a more accurate starting configuration.
To do that, use the normal Automatic solving mode for the dominant camera, and the Indirectly mode for the secondary camera. Assuming the moving camera path is reasonable, SynthEyes will solve for the dominant camera path, then for the secondary path, applying the selected camera/camera constraints at that time.
This approach will probably work better on shots where most of the trackers are fairly far from the cameras, and the camera moves a substantial distance, thus establishing a baseline for triangulation. If the camera moves (translates) little, you should use the Stereo solving mode.
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