Hey Wyatt.
I thought I’d share my technique for lining up orthographic images. I use Photoshop but I’m sure you can accomplish the same using any image editing app. The following pictures are from 3d.sk , an invaluable resource for references.
After bringing in my images, the first thing I do is create a new document that is twice as wide as my largest orthographic, then I copy both images into it. This gives me a little leeway on both sides and ensures I don’t inadvertantly ruin my original by saving over it (something I learned the hard way many times over).

Then I grab a guide from the rulers (CTRL-R to show rulers if they are hidden-click inside the ruler and drag to pull out guides). I also turn snap off (view menu). The first guide I lay out runs along the center of the front ortho. Using the Transform tool, I rotate the front view so that it is as vertical as possible.
From there, I line up the horizontal landmarks of the front ortho(eyes, ears, chin, top of head, etc). No face is in perfect symetry, so in the front ortho I focus more on the side that corresponds with the side ortho. In this case the left side of the face.
Now that my front ortho is set up, I start to tweak the side ortho using a combination of transform/free transform, liquify brush and perspective tools to match the landmarks as accurately as possible. I always end up with a tiny bit of distortion, but sacrifices need to be made because of perspective distortion.


One thing to note is that, depending on your orthos, you may need to do some editing on the front ortho beforehand to get it as symetrical as possible.
Before finishing this mini-tut, I’d like to credit the technique to my former teacher, Malcolm MacCleoud. I believe he learned it from Alex Alvarez personally over at The Gnomon Workshop where he did his studies.
Hope that helped.
-Rage