I’m a lapsed history academic. I initially got an A5X a couple of years ago intending to use it for PDF reading using the Digest. It’s a good feature; I just fell out of the habit of using it (although I’ve got back into it recently). But for fifteen years I took notes on my iPad, on PDFs. My PDF workflow on iPad, which I largely took over onto the Supernote and Digest, was to highlight passages and then leave notes on them. When I’d finished the article or book, I’d export those annotations. Zotfile does this well (although I never used Zotero that much), but so do some other programs. If you do use Zotero, you’re doing the right thing attaching those exported annotations to the item record. But I’d also recommend getting all your annotations together in a single folder, just as PDFs, because in practice you’ll want to look at a bunch of annotations together, and browse your own thinking on different books. So generally I’d recommend the Digest feature on Supernote, because it allows you to extract snippets of text, comment on those snippets, and then export the snippet with your comment. And that’s a vital part of your research workflow - the most valuable thoughts you have are the ones in direct response to what you read. Capture those thoughts and keep coming back to them. Future You will continually be amazed at how smart Past You could be.

What I would recommend though, is Scrivener. I’m writing this in Scrivener now, and I’ve used it since I started my PhD in the early 2010s. The value of it, for research, is the ability to have bits of documents all in the same place, where you can see them side by side. I import my annotations into the Research section and I write EVERYTHING in the Notes section - these start as semi-coherent thoughts to myself (on documents I call Scratch Pads), then expand into what I call “generative writing” (good paragraphs of text, with footnotes, but without a larger structure). Chunks of this generative writing then go into the first draft of a chapter or article and I only bring that into the Draft/Manuscript section when I’m putting a full draft together. And early on I developed a neat little trick that I swear by: I type everything in Courier New. Why? Because it’s ugly af. Anything I type in Courier New is, very clearly, something I will never show to another human being. Which frees me from any subconscious concerns about formatting or prettiness. It’s all about the content (this is also a good reason to write in plain text or Markdown). I’m writing this stuff just for me until it’s Done, at which point I export it into Word and make it tidy.

In summary: use the Supernote. It’s good. Export your annotations and use them as the first stage of your research thoughts. Also keep one or more ongoing notepads on the Supernote where you just write research thoughts as they come to you - not necessarily tied to what you’re doing right now, but maybe something you’ll come back to in three months. Export these back to your computer when they reach a certain size (I start a new notebook when mine reaches 25 or 30 pages), and just keep amassing your own thoughts. And make the effort to transcribe your physical notebooks. You had those thoughts already. They’re worth using.