Connect your atomic ideas and structure notes to add context. One generally starts with context (i.e., a specific course) and then adds notes in school. As you create atomic ideas and link them to each other, and structure notes, you begin to develop your topics and lines of thinking from the bottom-up.

remain empty or you can actually write something down or insert diagrams you

I previously shared Ivo Velitchkov’s 5-part series in Letter XXXII where he described in more detail his approach, and how he developed RIO (Roam Internal Ontology). Now, he has released the two ontologies he's developed (RIO and ROCO - ROam Core Ontology)