If I remember correctly, all you do is write the notes. They are there for the duration unless you delete or change them. If you change them you need to save the changes.
Originally posted by MCA depends on who's move it is:
if it is your move you write the note; make your move and hit submit -the note is saved when move is submitted
if it is your opponents move then you write the note and click the "save notebook changes" link.
additionally, if it is your move and you want to make a new note AND not move (to revisit the game again in a couple of days) - simply update the notebook, and click the move button WITHOUT moving any pieces. When you go back into the game (still your move) you'll see the notebook is updated.