Well, as far as I can figure it is the same thing we do now to modify and make themes. We use an html adn php editor and manually change stuff, image links, images, commands and so forth, this AutoTheme seems to do tell you to do the same thing. IT's a great tutorial though, the readme.
I thought it would be some sort of browser integrated program that allows you to go through each html and php,css files right there in th browser and adjust and modify them, but it appears not to be like that.

I posted over at the developer's site to see whats' up with it and if I'm missing something..we'll see.

mikem