I only take notes on papers when I read papers closely and deeply. I usually have the paper open in zotero and obsidian opened and I jot down notes as I read. I read papers for different reasons, sometimes for methods, sometimes for interesting results. I try to take notes on anything I spend time thinking about or want to remember, as “fleeting notes”. As I make notes, modular or not, Im trying to always think about connections to other notes or papers. This helps build ideas. Sometimes its obvious what the connections are — related papers, methods, etc. Sometimes its a random thought that reminds me of a completely different paper and I may make new notes to help flesh out these connections. Use the notes in whatever way is most helpful to you.
modular notes often emerge from these fleeting notes organically.
ive also been practicing reading papers using different lenses — see dumit styles of reading