Using post-it notes is the perfect technique to have more room for writing notes and still keeping them in your LDS scriptures. Just place the sticky side of the note along the margins so it doesn't cover up the text. This way you can lift up the note and read the text below. Some of the notes you could write are questions, thoughts, inspirations, coinage, lineages, travel routs, etc.
You can also cut the notes into smaller pieces (just make sure to keep part of the sticky side) so they don't take up as much room. This works well if you have a small question or thought.