From what I can gather, it’s a matter of stitching together Smart Objects and organizing them in a certain way. There are only 4 levels: Atoms, Molecules, Organisms, and Pages. Templates are left out because Photoshop (or any other static environment) can’t design with dynamic data.
Ultimately, I think Creative Cloud Libraries will be a nice enhancement for accomplishing an atomic design workflow in Photoshop.
I think it’s great to see designers working in Photoshop move toward crafting design systems in a smart way.