On the New Order page click on the upward arrow next to the submit button in the bottom left.
You can use the Notes box to add notes for the whole order
If you want to add notes to individual items of the order click the Item Notes button. A list of your items will appear enabling you to add notes to each item.
If you want to add a note for an individual item, click on the edit pencil next to the selected item in the order page.