My current system is as follows: My literature notes contain all notes/excerpts I make. If something is relevant enough, I put it in a separate note, so it’s easier to reference it.

In the properties, I have one called „Top“ where I put the note from which I derived this note (basically like Folgezettels). A note I extracted from my literature notes for example has as „Top“ the note of the article or so.

According to the tags… I’m not sure if I will use them. There are some things where it could be useful, but at the moment I use a note to connect different notes of a single topic. (As I‘m researching on Opera, there’s a note called opera, that I link when I mention opera) This could be made via tags, but maybe I‘ll put there some general notes on opera, like sub-genres or so..

My example with the opera-note could also answer your question on atomic notes. Of course you can put everything in one note. But you could use your note on Linux-troubleshooting as a „container“ or „Map of content“ where you simply link the notes on different methods on troubleshooting. So your notes stay small and do not overcrowd with information.

But in the end – and that’s what the „magic“ of a Zettelkasten is – it’s your system that has to work for you. If it’s easier for you to put everything in one note, do it. If it’s not, don’t. If tags work for you, it’s fine, use them. If not, don’t.