For objects one to several inches across, it is recommended that you control the spacing to within about 1 mm. Control of the background, for when the subject does not take up the entire field of view. With focus at macro distances, distant objects will be badly out of focus. You may also want to allow more depth of in your subject by eliminating points at infinity. Some pieces of cloth can serve as a background, eliminating infinity objects in the final image.
Proper lighting is important.
In macro stereo photography, it's usually desirable to get the depth of field as great as possible, so you will usually set the aperture fairly small. To get reasonable exposure times, you therefore need a very bright light source, for example natural sunlight, bright lights, or a strobe. If you use a flash, it is important that the flash not move between exposures, as this would cause the shadows in the two images to not match.