One of the ideas that Sascha and Christian of Zettelkasten.de have espoused is not not giving too much structure up front. At first I flirted with the idea of markdown files, and using something like an extension to Jekyll to resolve links and generate an HTML render of my zettel archive. But that's the same mistake I always make :) Way too much for what I need.

Like you, I settled on just using a text editor (sublime text and atom) with Markdown files. I don't plan to render them, I just like the syntax highlighting.

I think your proposed system captures the important part of the knowledge intake, ie two levels of abstraction (writing a source note, and then connecting the new knowledge from source note to (or just dumping it in) some existing node.)

But one other idea from Christian and Sascha is to avoid folder structures, and allow the organization to develop over time. On a work topic, notes from a few guidances and presentations, plus my experiences, cluster to create a note which transcends a categorical boundary I would have erected with a folder structure.

So, the suggested alt strategy is dump everything into one folder and create clusters using other structures, as they reveal themselves to be useful.