Thank you for those tips, they gave me something to think about with regards to “ongoing” notes.
I guess the only issue is that when you mark an ongoing note “done”, it shows up in the timeline on all days it was assigned to, even though I haven’t touched the project on those days. It’s important to me that each day in the timeline reflects all I did across projects, and not just what I had on my roster. I guess I could just change both dates when I mark it done.
Thanks to your advice, another way to address my situation could be to never have fresh notes assigned for today, just have all the “candidate” tasks on the agenda, and if I did something today, then set that note to today, mark it done, and remove from agenda.
With this approach I guess I could get used to pressing ⇧⌘ ⏎ and ⌥⌘ ⏎ to complete a note. 
I like having that option, but right now I’m trying to stay careful not to overcomplicate the process until I absolutely need to. 
I’m expecting a good use for tags to emerge naturally with time.