I agree it gets overwhelming always looking at different tools and a source to fuel my procrastination. Now the things I have settled on are typically supported on the Mac, iPad, and iPhone. DEVONthink excels at allowing me to find my information on either platform. I use TextExpander for some markdown items like checkboxes and image links, that way the same command is available to me in Sublime Text 3 on the Mac or Textastic, and Drafts on the ios devices. I have PDF Expert for both iOS and Mac, but I’m starting to replace that with MarginNote 3, which is similar to LiquidText in that you can add notes outside the page boundaries, but can do a whole lot more if you can get used to the UI. I think LiquidText is much more intuitive, but what sold me on MarginNote 3 is the ability to have highlights added as color coded nodes in a mind map. MarginNote 3 is not the best mind map program out there, but it exports to iThoughts which I have used for years on both iOS, Mac, and Windows. MarginNote 3 has a Mac version too, so I find that easier to use when rearranging mind map nodes on the large monitors attached to the Mac. I had ended up with a complex workflow for PDFs with Zotero, ZotFile, PDF Expert, Box, and DT. I picked Zotero for ZotFile had the ability to extract the color highlighted text from PDFs into notes. The problem I had was I had to manually run the extraction and then run a report in Zotero to get the notes into DT. MarginNote 3 simplifies this process for me by interactively extracting those highlights into the mind map and/or outline which can be shared to DT as a PDF with the option to include the just the highlighted pages of the original PDF or all the pages. The nice thing with PDF Expert is that have a Keyboard Maestro macro that I can execute while selecting an item to read in Zotero that would create an OmniFocus repeating task to open PDF Expert with that PDF on either Mac or iOS.
Unfortunately PDF Expert does not support their own URL scheme with the Mac version, but you can launch the default app with this link. This setup leverage ZotFile for Zotero to use my Box folder for PDF storage and PDF Expert could be configured to sync Box on iOS. That allowed me to annotate on any device, as long as I gave it time to sync. I primarily wanted to annotate on the iPad Pro with the pencil and be able to find the results in DT or send an attachment.
MarginNote in this case would have to import the PDF into its store that it syncs via iCloud to other devices. That changes things in that Zotero will not have the annotated version
------------Links to shared PDF document on Box for PDF Expert Mac and then iOS----------
I just tried a test with MarginNote 3 which is to backup a study notebook and chose clip to DEVONthink on my iPad. I went to the DT Inbox where it was imported and not surprisingly it is there, but cannot be viewed within DT. I can however share from DT to “Copy to MarginNote” and it others to Merge or Replace the existing notebook. I did not test any further than that.
I think exporting as PDF to DEVONthink is better in that it gives you the ability to search for keywords and on the Mac version be able to leverage the “See Also” feature to find related items. Once I see it is MarginNotes or GoodNotes and need to continue to edit the document, then I can go to the right application to edit. For me, the problem was finding out where I had something before I got DEVONthink. I would search email, Slack, iThoughts, FreeMind, Notability, Box Notes, etc.
You could always try to export both the native and PDF versions to DEVONthink and group them together, but that is starting to sound too complex to maintain consistently.