Niamh,
Within the
Family Tree Maker, current versions back, you need to Copy/Paste or Type in Source information into the Notes section. You can not link Source information into the Notes field.
I don't know about your notes, but my notes have many sources, so the Notes field can't have a source OR you wouldn't be able to identify what piece of the Notes was from what source. So the way to put source information into the notes is by Pasting or Typing.
You also have be be consistent as to where you put the source information, at the beginning or end of the text within the notes.
Russ