Hey, Abazu!
I’m going on a similar journey with Obsidian right now and I found it helpful to sort of map out how I want to talk to my second brain first: Input (random note, meeting, presentation) → Area of Development (process:process category, skill:skill category, etc.)/Project → Output (reference note within the system, project document, etc.).
This allows me to understand and see the journey of my thought process, allowing for an end result, while still being able to, at least at a high level, use a Johnny Decimal system to keep things organized.
Section 1 in my attached image is what the flow looks like, as a whole, with an Example of my game projects being used in the bottom left hand corner.
Section 2 is my structure in Obsidian (Please note the numbering has not been updated and every subfolder is starting at 10).
This allows my 20 Area of Development to contain buckets for more developed notes before they are connected to more finished notes associated with a final resource or project as seen in Section 3. I can have infinite notes and rely on my note’s zettlekasten’s properties to create the appropriate connections, which I show in Section 4.
tl;dr: do you want your system to support the development of your second brain or group your process together with your final output? I believe answering this will help you structure your system.