I recently tried stereo imaging with some good success and discovered some ways to do it in photoshop in 1-2 clicks.

www.renderosity.com/mod/gallery/index.php

how i did it was quite simple i set the camera (poser, though the same can be done with vue.) to point at the girls hips, face would have been fine for a straight angle or isometric angle.
I took the left eye shot then moved the camera .700 to the right to approximate the distance between a humans eyes. then shot the right eye render.

open photoshop and open the left eye render first then open the right eye render and paste it to a layer on top of the left eye render. Here was the trick since my 3d glasses had green(left) and cyan(right) I turned off the green channel on the top layer (right eye layer). that was all i had to do...
since i had the camera pointing to the subject I did not need to realign any of the layers. and because I use both a right and left eye render the differences in the image were where they needed to be.

an important note to think about is the type of glasses, if the glasses used are left red and right blue then you will want to turn off the red channel on the top layer. for the image to work with your glasses. for those with such glasses turn them upside down to view the example.