As explained in the metadata section, you can attach custom metadata to almost every Atoms entity.
Tou can add metadatas to your joints is by adding new attributes on them. You can do it when exporting both a skeleton definition and an animation clip file (fbx or atomsclip).
Any attribute with a name starting with "atoms_" that you add to a joint in Maya will be added as a new metadata to that joint in your skeleton definition or animation clip.
Please check this python tutorial if you are interested in knowing more about this.