I’ll take a stab at bookmarks.
Bookmarks are links to other documents, and those documents fall into 3 categories: Documents within the same Scrivener project, external website URLs, and files on the same computer that are external to the Scrivener project.
A bookmark to a document in the same project will display the contents of that document in the pane below the bookmarks in the Inspector. If the document is a Scrivener text document, you can also edit the text there. If the document can be “displayed” in a Scrivener editor but not edited (ex: PDFs, sound files, web archives), then you can still interact with those files in that part of the Inspector.
External websites just load as a web page. This functionallity is somewhat limited, as Scrivener doesn’t contain a full-fledge web browser, and so may not be able to render a page well, or get past the logon screen. You can double-click on the bookmark to open that website in your default browser, however.
External files on your Mac are the third kind of bookmark you can make. This is the most fragile kind, and the one I’m least familiar with. I think that it can’t track re-names or moves of the bookmarked files, so I tend not to link to external files. External files can also include URLs that other programs provide, including Scrivener links to specific documents in other projects. If you use the Edit/Copy Special/Copy Document as External Link menu in one project, you can paste that string into the link field when creating an external file bookmark; when you then click on that bookmark, it will open that project in another window, and open the specific document in an editor within that window.
I use the first kind of bookmark all the time. It’s quite useful for fiction–if you keep documents on each character, you can bookmark that character’s document in each chapter they appear in, adding notes about that character as they emerge in the telling of the story. In this way, bookmarked documents are often better than document notes, which are only visible when you are editing the document they’re associated with. The same character info may be useful across several chapters.
I’m sure there are similarly handy note-taking applications for use in writing non-fiction.