I then save it as a .jps (a jpg renamed so that stereo software can identify it). The resulting image looks like this:
I then use the flash viewer from StereoPhotoMaker
to display the images. Although this is a nice bit of software, I just use the flash viewer and have a Perl script which applies the mask, and then the webpage is stuck together with php. It also writes the manifest and thumbnail pictures for the StereoPhotoMaker viewer.