There are many ways to approach database organization and handling notes and comments about documents within the database – depending on personal preferences and workflows.
Personally, I prefer not to modify my original documents, but to create rich text documents that hold my notes and comments – often, I may associate multiple such notes documents to a single source document.
I may “associate” a note to the reference document by using the same Name, with additional text. So if I do a Lookup search on the reference document’s name, the Search window will show me all the notes I’ve created about the reference document.
Or I may create a link in the note to the referenced document, by selecting some text, Control-clicking on the selected text and choosing the contextual menu option Link To… That let’s me “jump” to the source reference by clicking on the hyperlink.
I usually organize my references into conceptually related groups. But when I’m working on a project, such as writing an article, I’ll create a new project group. I may replicate some of the more important references into that project group, perhaps into a subgroup, or duplicate a reference into the subgroup if I plan to “mutilate” that copy by inserting highlights, markups or adding notes to it. If I’m going to insert keyword tags into the Comment field of a source document, I’ll usually do that on a duplicate copy within my project group, as that tag is probably going to be highly specific to the project I’m working on, and probably irrelevant to the next project for which I might use that reference document.
When I start a writing project, I’ll usually start by creating a rich text document in which I lay out to myself the purpose of the project and then the principal sections of the product in semi-outline form. For each section I’ll include notes about what it should contain, and perhaps important references materials are listed. I’ll create hyperlinks as I go, so that this document becomes a working record of the project (eventually, a sort of table of contents of the draft sections) and from it I can quickly “jump” to the draft sections of the article, references, and so on.
But that’s just the way I like to work. I like to do my draft writing within my database, where all the references are at my fingertips and I can use features like See Also or See Selected text to fish for ideas. Others have different working habits.