My structure is evolving because my source material comprises many different types of inputs and I've only been working on it for a few (relatively) months.
I have web page archives, some plain text, some rich test and some markdown files, PDF files of misc info, PDF files of scientific papers (usually with a DOI number), Kindle books bought from Amazon, Kindle books bought from other sources and Kindle books from free open source places like GutenBooks, paper books, paper handwritten notes on paper or kindle books, digital GoodNotes notes on all source types, kindle highlights, quotes and notes in all ebook types and more. I am slowly evolving a system that has specific workflows for all those inputs into my own personal knowledge management system which I am implementing in Obsidian.
I am developing templates to collect the basic information on the input that is the start of the note. So for example I have Zotero as a bibliographic system which is the repository for all my scientific papers which are nearly all PDF files. I annotate those items on my iPad in Highlights and I use Zotfile and MDNotes to incorporate my own thoughts on the quotes and useful information into a format that can be imported into Obsidian using the Citations plugin. From there I can link and correlate to my hearts content.
For kindle books purchased from Amazon I make my annotations, again on the iPad, in the Kindle app. I am trialing the Readwise Obsidian plugin and the Kindle Highlights Obsidian plugin to get those items into my Obsidian system where I am starting to use the Obsidian plugin Quick Add to transclude the notes into separate files where I can exppound on my own personal thoughts while still keeping the original annotations intact in a single file, one for each book.
For kindle books purchased from other places or open source I am still stuck. There is no good way to get the hihghlights and annotations out of those into any form I can use.
For GoodNotes handwriten notes, which are typically for seminars, webinars, training courses and events I am using a shortcut on my iPad that first does handwriting recog. on my GoodNotes files (for my scribbles it's about 95-98% accurate) then does an export into markdown and automatically saves the resulting file into my Obsidian inbox where I can then edit it to correct the handwriting recog. and add it to my notes.
For paper handwritten notes I am reviewing them. Really important ones I am re-typing into Obsidian. Les important but still ones I want to save are being scanned and stored as attachments in Obsidian.
I am making extensive use of MOC or TOC type notes in Obsidian that are my index to my ever growing pile of stuff and I am making use of the local graph display and find unlinked files plugin to locate orphaned files and decide where I need to connect them.
It's an evolving process and I'm finding the more of my backlog of notes and info I get into my Obsidian system the more useful the entire set of stuff becomes.
PS edited to correct typos because I saved this note into Obsidian as a short for of my workflow and realized I had many spelling and punctuation errors.