For passive polaroid stereoscopic projection (see examples here) there are a few different ways the computer and graphics card can be connected to the projectors and monitors. The following assumes an XGA stereoscopic system but the principles apply to higher resolution displays. Three approaches are illustrated below, each has it's relative merits.
From the software perspective option 2 and 3 appear identical. The software only sees one display even through it is a mirror pair.
Option 2 is interesting in that it can be used with a laptop which generally only have a single video output port.
The main difference between option 2 and 3 is simplicity at a higher cost. That is, option 3 has fewer components but displays capable of at least 2048x768 are somewhat more expensive than two video splitters/amplifiers.
Option 2 has some significant advantages over 1 for some operating systems which require special window manager calls to open a single window fullscreen across two displays. Option 2 presents a single display to the software and thus there is generally wider range of tools that can be used.