How can I align photos for stop motion?
To ease in the alignment of the photos, you could use something like Anazi Stop Motion Animator.

It has an "Onion Skin" feature that allows you to see two different frames at the same time to help in aligning them.

You may find some good advice on how to use this software or what software others are using for this by searching for some stop animation sites.  The only site I have personally seen is brickfilms.com which is a stop motion animation site specializing in animating LEGOs.  On their resources page you might find some helpful advice.