Dan Sheffler, who you might know for his valuable comments on this site already, has an interesting workflow: first, he captures ideas in a study log while reading; then, he picks the gems and writes Zettel notes later.
This difference of “engagement notes” and “memory notes”, as he calls it, fits the Zettelkasten method well.
“Memory notes” are Zettel notes: they are the essence of captured information.
“Engagement notes” are a replacement for what I’m doing when I scribble paper notes on the go. Paper notes are temporary. I toss them away.
Using a notebook as a study log like Dan does works well when you are working at a desk. These notebooks may become something to keep around and show to your grandchildren.
Just look at the beautiful image of his notebook now.
Update 2015-08-12: Dan uses “engagement notes” as a theoretical term; PDF annotations are engagement notes just as notes on paper or in notebooks. It just turns out he likes using a notebook best.