New user: using DTPO, Bookends, and Omnioutliner with PDFs

I’m using DevonThink for a project for the first time. Right now this project involves going through a bunch of scientific PDFs, outlining them, and trying to identify patterns. I’ve been reading and annotating the PDFs in Goodnote, storing these annotated PDFs in Bookends, and outlining what I find in OmniOutliner. All my PDFs, which are stored on a cloud drive, are indexed in DevonThink, and I’ve been copying the relevant ones to a database associated with the current project.

I’d welcome any advice on how best to use DevonThink for my project, and also would like to ask two questions.

  1. If I import Bookends references into DevonThink, are they updated as I add notes in Bookends? If not, is there a way to index Bookends references rather than import them?

  2. In OmniOutliner, I have been putting links to the papers indexed in DevonThink. What is going to happen when I sync DevonThink and OmniOutliner (via OmniPresence) to another computer? Will the links be invalid?

How would you proceed? Right now DevonThink is the lease useful member of the trio of software I am using. But I expect I need to learn more about how best to utilize it.

Importing the references again updates already imported items. But that’s not performed automatically.

x-devonthink-item:// URLs don’t depend on the actual path, the links will be still valid.

Might be useful - [url]Put up Example page]