The first hing I need to understand is how I will look for things. My initial impulse is always to go to search first. This means my organization, if it is to be of any advanced form, must serve another purpose than helping me find what I'm looking. Here I defer to the Niklas Luhman's idealogy behind zettelkasten: to make connections that are not obvious to my mind. This is best done by linking.
What I have learned is that I am not the note-taker who will sit down and do all of this up front. I have tried this and instead end up with a backlog, which is far more detrimental to my system than not having links. It is however important that I take the ideas I have highlighted in books and summarize them in my own words. I do not have a natural inclination toward this either but adding concepts into my system that I cannot articulate and therefore do not understand fully are of no use to the system. I must therefore commit to summarizing the points I find the most interesting as my fascination will motivate me to go through the process. But, I also have to accept that this means leaving other ideas to be deciphered later.
Overall, as much as I like the idea of creating atomic notes, I find that the process itself becomes an obstacle to me creating and thinking deeper. I get caught up in the chore of it. I will then rely on Fleeting/Literature notes as my primary notes and will only create atomic permanent notes when I feel it's absolutely needed. To my system, I will also add the crucial use of the random button to pull up arbitrary notes on a daily basis. I will attempt to make any links that come to mind and summarize any unsummarized ideas that catch my fancy at that time.
This methodology will not satisfy my OCD tendencies but it will allow me to focus on more important things like using the information and ideas to create something rather than spending countless hours organizing notes as if that itself is the important process. I also think that I should dedicate myself to going over my daily reading at the end of each day while things are fresh. This too will prevent backlog. I will use the Konick method of headers for the page numbers and the summaries underneath.