I had similar difficulties. (Especially with the naming convention. The Zettelkasten method makes sense to me for numbering cards you have to keep in a box. It doesn’t make sense to me for notes that are in a database where you can tag them with multiple things.)
With regard to atomic notes, though, I eventually figured out that none of my notes were that BASIC. It was as if everything I had was at least a “molecular” note, and I’d skipped right over the atoms. Which is totally fine, at least to start with – but was helpful to realize, as it helped me know what the missing piece was if/when I was struggling to link notes together. Sometimes the problem was that the “connection point” didn’t exist as a note in my vault because it was so simple I just take it for granted.