The 'Author-it Honeycomb source' means the hv_src folder. This folder contains all kind of settings for the lay-out of the Author-it Honeycomb output. For that reason, we can also refer to it as 'Author-it Honeycomb template'.
Hv_src contains everything except the core application (the js folder) and the published data.
Create a copy of the Author-it Honeycomb source for every theme/lay-out that you want to create.
To process the output correctly, the Author-it Honeycomb source must be included in the Author-it output. It is copied to the publishing folder with a Before Publish Action in the publishing profile.