It can be messy to think about where a digital notebook fits into everything. I just embrace it as another place to sketch and don’t expect it to do reminding or organizing work. I have a Siri Shortcut on iPad that opens a specific Goodnotes notebook for me. That gets me using it often enough. If I’m taking action-oriented notes in Goodnotes (not typical), I put any tasks/followups elsewhere immediately afterwards. If I’m making something to share (e.g. a UX diagram that the team needs to see) I export the page or share a screenshot to that other place and just leave the old one in the notebook. Flattened PDF archive into DevonThink, but I don’t do it before the document is done. I don’t delete the document afterwards because there is no risk I’ll accidentally add to the wrong one (so far.)
Also, if you’re often wanting to make notes that will end up in DevonThink, you can make them directly in DTTG3 in New > From Template > one of the blank PDFs. It doesn’t have as many tools, but all your sketching and note-taking will go directly to your database and won’t add an irrelevant page to an existing notebook.
Again, messy. Curious where you end up.
Edit: Notes also works well for quickly creating an item you want to share/store elsewhere, and IMO is quicker to clean up than Goodnotes, especially as you can quickly do it from your Mac.