Having an outlining tool (like logseq) as a column left to main text.
Like a commenting column in Word, this could serve as an outlining and commenting column next to the main text.
Folding and unfolding of the outline column would keep the main text clean, as I can put my messy thoughts and links into the outline.
If the headings of the Outline are linked to the headings of the main text, and kept at the same level, you would always have the right information next to the section you are focusing on.
It would be similar to the commenting feature in Word, but combined with outlining.
What I would do then: Whenever I would create Literature notes, I would create block references to the quotes in my outline. And then when I would come to writing the text, I would have an outline with references ready.