I also found myself grappling with this, but I’ve managed to find a solution.
Personally, I find it doesn’t always help to be strict about categorizing without any duplication or omission. If something fits into two categories, why not duplicate it? Taking notes is a tool for my own memory and reflection, not a showcase for others. So, don’t sweat it, go ahead and duplicate where you need to.
I dive right in and treat a whole to-do as a single project. You probably think I’m crazy, that would make Agenda’s sidebar overflow. But I’ve found that it actually won’t. I quickly found that some to-dos were actually subordinate to others. This way, I swiftly identify the key to-dos in my life.
Every 3-6 months, I will export some projects that I no longer need and put them in Notion, which I use as a repository to store some cold data. And in the local app, only the data that I am working on recently is stored.
I don’t know if this is the fact, but I have a distinct sense that Apple style apps don’t seem to be designed for infinite amounts of data like Windows style apps are, instead, they are designed for the moment and finite data. Just as a person’s stomach, although there is a lot of food, there is a finite amount of food needed.
These key tasks could be super important things, or simply tasks that are a little challenging for me. Emotionally, it feels like hitting a wall sometimes, not being able to do things as well as I’d like. In these cases, I create items and categorize them according to the key difficulty, like goal-oriented, preparedness for something, outdoor stories, reflection, need to track, making a decision, not the actual category they fall into like travel, research, cooking, or work. Of course, most projects are not categorized and exist among Other Projects. This helps me look back and reflect, as well as build and maintain new habits.
I only jot down things related to Actions or Events on Agenda, leaving the info-level stuff for apps like Obsidian. Things like my research, daily running logs, observations, and other informational items live on Obsidian. If I need to build an article, I turn to Ulysses. For documenting special moments of my moods and feelings, I’ll use Dayone and Photos. In short, take full advantage of the unique strengths of each app and don’t get hung up on implementing everything on one app. Some stuff is hard to separate, so in those cases, just copy-and-paste! In my opinion, the brain is the best tool for integration. The brain registers the context of something, such as smells, environment, colors, sensations, and the multitasking you are doing at the same time. And, of course, the brain tends to structure things, so try using @object to refer to a noun, such as @Ratatouille (food), @Dead-Poets-Society (movie), @explore (approach), @Grand Canyon (travel), @Algorithmic Symphony (project). I would use Notion to set up a home for these Objects. Then set properties, and categories, adding backlinks. I named the database Object Contacts. You can read this post of mine.
I review the Today Overview to get a complete picture of my day, which means there’s no need to create a Daily Note. If I’m working on a particular note today, as I was yesterday, I’ll extend a day to today for the assigned date. If a note is ignored, it will stay at the last date. The great thing about this is that I can clearly see where I tripped up and moved on, instead of having a note get lost in the depths of my memory because I paused for a day. Of course, a small percentage of notes are scheduled, and I’ll make a note amongst the notes on whether or not I worked on this note on that day.
Hope these helps 