I only save MarkDownload article grabs as full articles into that source folder. For PDFs (which I deal with rarely) I use Zotero and then copy a reference + Zotero link into Obsidian as needed.
My own notes go into a “Notes” folder in Obsidian, covering my own thinking, and notes/highlights (“literature notes”) broken by topic which may come from various sources. For the latter I will include a link to the source folder article or Zotero, for example. I’m not too anal about it, I find I only go back to those sources while I’m actually writing a note, and not so much later when I’m reviewing my own notes. But my workflow doesn’t demand meticulous citations, its really just for my own benefit/OCD.