The manual suggests that you can:
Using Notes, Highlighters, and Collections
»»Return to the Bookshelf by tapping the Collections button at the top left.
»»Add highlighters by tapping the highlighter icon in the top left corner of the Collections window.
»»Make notes by opening the book and naviwgating to the text you would like to highlight.
»»Hold your finger down at the first word of the text.
»»After it is highlighted, drag the highlight to the full group of text you need highlighted.
»»Tap the section once, then tap make highlight.
»»If you need to add a note to a highlight, tap again, then tap make note.