My Obsidian vault is divided into two general areas: Projects and Knowledge graph. For a certain subject, I create a folder called ‘literature’, where I put in the exported highlights of the papers I read.
So my workflow typically involves reading a paper and highlighting generously, then in the left side panel in the paperpile online reader, select export then markdown then copy, then paste the highlights into a note in the appropriate literature folder in obsidian. Then I copy link from the reference in paperpile and paste it into the same note in obsidian.
That way, while writing in obsidian, I can reference either a highlight or the whole note all the highlights. If need be, I can use the link to jump straight to the paper in paperpile.
Hope this is clear enough
Best,
H