Thanks for your help Hutch and your patience trying to fathom my mixed up thinking, its because in writing apps I can do lots of fancy stuff, but I am learning that kindles and e-readers are extremely basic.
The notes popup works fine, but at the bottom of the page there is a whole section of notes which supply the popups, so when the reader reaches the bottom of the chapter, they will see all the notes, which are nothing to do with the narrative.
I was wanting to hide these notes, so that all you see is the actual chapter text, but still have popups
I cannot figure out how to hide the notes section, so I have now simply put a heading 'Notes Section' above them
If you could tell me if it is possible to hide the notes, then that would be great, if it is not possible, I will settle for the heading 'Notes Section'