We check if what we understood from a text is really in the text by having our understanding in written form in front of our eyes. We learn to focus on the gist of an idea by restricting ourselves in terms of space. We can make it a habit to always think about what is missing when we write down our own ideas. And we can practice asking good questions when we sort our notes into the slip-box and connect them with other notes.
Asking if we really remember the thing we take notes on correctly, asking what (information) is missing and asking other good questions is party of the discipline needed to get the most out of the notes we take.