The other parameter is the distance from the eyes where the lines of sight for each eye converge. This distance is called the fusion distance. At this distance objects in the scene will appear to be on the front surface of the display (``in the glass''). Objects farther than the fusion distance from the viewer will appear to be ``behind the glass'' while objects in front will appear to float in front of the display. The latter illusion is harder to maintain, since real objects visible to the viewer beyond the edge of the display tend to destroy the illusion.
Instead of assigning units to it, think of the fusion distance as a dimensionless quantity, relative to location of the front and back clipping planes. For example, you may want to set the fusion distance to be halfway between the front and back clipping planes. This way it is independent of the application's coordinate system, which makes it easier to position objects appropriately in the scene.
To model viewer attention realistically, the fusion distance should be adjusted to match the object in the scene that the viewer is looking at. This requires knowing where the viewer is looking. If head and eye tracking equipment is being used in the application finding the center of interest is straightforward. A more indirect approach is to have the user consciously designate the object being viewed. Clever psychology can sometimes substitute for eye tracking hardware. If the animated scene is designed in such a way as to draw the viewer's attention in a predictable way, or if the scene is very sparse, intelligent guesses can be made as to the viewers center of interest.
The view direction vector and the vector separating the left and right eye position are perpendicular to each other. The two view points are located along a line perpendicular to the direction of view and the ``up'' direction. The fusion distance is measured along the view direction. The position of the viewer can be defined to be at one of the eye points, or halfway between them. In either case, the left and right eye locations are positioned relative to it.
If the viewer is taken to be halfway between the stereo eye positions, and assuming gluLookAt() has been called to put the viewer position at the origin in eye space, then the fusion distance is measured along the negative Z axis (like the near and far clipping planes), and the two viewpoints are on either side of the origin along the X axis, at (-IOD/2, 0, 0) and (IOD/2, 0, 0).
