References, which includes x-rays, are kept separate from the Zettelkasten.

So what I do is I read and create an x-ray of a certain article, book chapter, or whatever. And then, when I have the x-ray, I go through it turning any worthwhile ideas into atomic notes, which are then connected to other notes.

You can think of it as plugging ideas out of the x-ray and inserting them into the right place within the Zettelkasten :)