Here is how to make a Red-Cyan Anaglyph from a stereo pair that has already been aligned to the window.
I personally don't like to use Anaglyph glasses, so I align my images using the techniques described on the alignment page,
then I use this technique to convert them to an Anaglyph. This technique is also instructive because it gives you a good
feel for how an anaglyph image works.
We start with the left and right images already loaded into separate layers in Photoshop:
If you want to use anaglyph glasses to see your alignment work in real time, then
check out this tutorial on how to use Advanced Blending: