It's quite simple: every set of notes has a "header" and a "body".
For the header:
Every page in your set of notes must be marked with your initials and a document number, and every page must have a page number and the date. Multiple pages should share the same document number if they concern the same collection of ideas, though they don't always have to. A general rule of thumb is one document number per set of pages written in a single sitting, plus additional pages written to extend or ammend the original ones shortly after they were written.

For the body:
The body should consist of a set of numbered paragraphs or sentences, the numbers showing the order in which they were written. If you change your mind about an idea after writing paragraph or sentence, or want to comment on it or extend it, you can attach a note directly underneath it with the same number, plus a dot and then a new number for the note.

E.g. if you have statement A with number x; the first comment on A should have number x.1, the second should have x.2. If you want to comment on a comment, you use numbers like x.1.1 or x.1.2