The notes are loosely informed by Daniel Kahneman's excellent book1, Thinking Fast and Slow.
If you are at the point of still deciding the broad area of your topic then almost anything is worth paying attention to. We tend not to do that however. We each bring to this task a history, a set of built-in ways of making sense of the world that predisposes us to pay attention to some things and not others2.
Skimming a paper and asking is this useful for my issue is probably what you'd call a fast read. Here, we pick up clues that may suggest the paper is too removed from what we imagine our issue will develop into. The only problem with this is that you can filter out useful, albeit contrarian positions or perhaps ideas that others have not associated with your issue. It's not an easy balance to achieve. In many respects, everything you look at could potentially be useful but you don't have the time to to a slow read on everything you come across.
The place to write about your thinking and filtering is, you guessed it, in your 1st notebook.