So here is how I have things organized.

Literature is in my Calibre Library, under a virtual library.

This zettlr_orbits is supposed to keep track of my thoughts and writing as I go.

The Folder structure is as follows.
./ ## Contains Everything 
    zettlr/ ## Contains my knowledge base on the topic
    Writing/ ## Contains my past written work on the subject.
        CurrentWriting ## Includes any current presentations or papers I'm writing
        YYYY-MM-DD_type ## The generic style of my presentations etc. Once in a written state
    Code/ ## Contains any code I've developed spedifically for the project.
    
This is all going to have version control using Git