Although it is possible to use Stereoscopic 3D to increase the "presence" feeling in your simulations, this is not something we would recommend. As it stands today, this technology can give very different results - even exceptional ones- but the cost for such feat may well be ... physiological. The Stereoscopic 3D as we know it may accurately be described as a human visual sytem "hack". The underlying principles of this technology have not changed since early in the twentieth century.
All the relative failures of 3D TV screens, Nvidia Stereoscopic goggles or even Nintendo 3DS bring some credence to the claim that this technology has yet to attain its mature state. Only the movies industry can still (for now) claim a solid advantage with this technology for some very well executed titles (Avatar and Gravity come to the mind), which do not take an important physiological toll during the experience. This excellent article lists the deeply rooted reasons playing against Stereoscopic 3D taking off. http://www.dr-lex.be/info-stuff/3dfail.html