The most common advice on this is probably “just do it, bro” / write first, organize later.
But I’ve always found that overwhelming. Especially if you have a lot of data already to document, you can end up focusing too much on the macro “what goes where” and too little on the micro “making stuff sustainably usable.”
I would grab a real life notebook and start brainstorming what your personal needs are first. What information do you need to store? What info do you need to access rarely vs often? When and how do you need to access it? Work from broad ideas down to specific things you can implement. Doodle templates, whatever you’ve got to do.
(If that sounds like too much work, there are demo vaults floating around you could start with. Maybe someone here can link a list of them if you’re interested.)
Then take a specific project or use case and implement those systems in Obsidian with it.
When that inevitably fails / you realize some facet of the system fundamentally doesn’t work for you, figure out what the issue is and make any changes needed; rinse & repeat. Eventually, you’ll get over the hump and be making more notes than organizational tweaks. That’s when you start moving all the similar projects / workflows to your vault.
YMMV, but that’s the process I’ve found the most practical when getting organized and switching between tools over the years.
When you’re brainstorming, by the way, consider how you’re going to minimize duplicate information and conflicts. That’s one of Obsidian’s strong points thanks to links and note-in-note embeds. And look out for more obvious edge cases, like how you’re going to handle notes that fit in multiple categories; these help reveal major structural issues that would otherwise slip by. Consider that Obsidian has lots of different ways to group content (like tags, metadata, folders, and links) that can be mixed & matched.
One last tip: It’s fine to have multiple different systems and areas for doing different things with your vault. Top-level folders are good for creating these kinds of divisions.
You can make a folder where you dump things you currently want to jot down in that “just do it” style, for example, to get into the habit of using Obsidian and develop a better sense of what content you have to organize. And then have a different folder for trying out possible structures in more depth etc.
I like having a section that breaks my normal category-id rules, specifically for brainstorming and ideating. Others like having a section for daily notes or their zettelkasten. When something comes up that doesn’t fit your structure, it doesn’t have to be shoehorned into what’s already there, if you don’t want it to be.