I want to manage my references within Zotero, because I want to do a dissertation using Markdown and the reference manager. I have done this tutorial (https://programminghistorian.org/lessons/sustainable-authorship-in-plain-text-using-pandoc-and-markdown) and it had this:

"The general idea is to keep your sources organized under one centralized bibliographic database, while generating specific and much smaller .bib files that will live in the same directory as your project. Go ahead and open your .bib file with the plain-text editor of your choice."

So I tried to manage my references by using topic-based directories and then I exported each directory as a separate Bibtex file. I added two different news articles from the same site and they are written by the same author, and when I looked at the IDs within two Bibtex files, they had the same ID. So I decided to just highlight all directories (by clicking on a top directory to collect all references) and then export them as one big bibtex file and that sorts out ID duplicates.

Is my above method the best way to manage and create the bibtex files or is there another way of doing this better?

P.S. I have written a Python script that appends a name of a bibtex file before ID key value. Thus, it's possible for me to know which file a reference came from and prevent possible duplicate IDs. However, I still would like to know your suggestions as to how to tackle the issue.

Thanks for reading.