How do I add notes to items in the scatter plot?

You can add named tags and tag items using different symbols, or add written comments and conclusions to them.

Click an a circle - an item - to select it. You can select multiple items by shift+clicking. Once you have selected an item or items, you can tag or untag them and edit their conclusions.

See here on how to create tags and tag items.

See here on how to add conclusion fields and edit their contents.