The way that worked for me, was to use Trello to create a skeleton of my areas and categories. That way, I can move the cards around and easily add new cards and visualise the whole thing, kind of like a wall of paper post-its:
The second thing I did, was go for quick wins. I knew my gmail inbox was messy with thousands of unread emails. I used my new J.D. system to delete lots of old filters and create new ones, and create some proper structure to the labels. Now I mostly have inbox zero, just need to clean it once a month. Once I did my inbox, it gave me more ideas of what was unnecessary areas that I just copied from other users, and what actually worked for me.
Next I did my file system, now I’m doing photos. Next is migrating from Onenote to Heptabase.