The iBooks app for iOS (free) is a pretty good eBook reader. Is it the best or most feature-rich reader available? Not necessarily. Apple definitely took a simplistic approach with their reader, and I think it was the right decision. I like clean apps, and sometimes, too many bells and whistles can complicate things unnecessarily.
One of the features that I really like in iBooks is the ability to create notes. This is especially useful when viewing textbooks or using it for studying. Using notes is simple.
In this example, I will open Walter Isaacson's book titled "Steve Jobs". When I come across a line I want to make a note about, I simply highlight the text, then tap the "Notes" button.
From here, I will type the notes that I want to make related to this line.
You'll notice that once a note has been added, the text will be highlighted and you will see a small square to the right of the text. This indicates that there is a note available.
To view the note, simply tap on the note icon. If you want to edit the note, simply make the changes in the note field.
If you want to view a list of all notes available in this particular book, tap on the content icon in the top left corner (next to the "Library" button). This will reveal a list of chapters, bookmarks and notes. Tapping on the "Notes" tab will show you a list of all notes within the book.
To delete a note, swipe to the left on the note you want to delete, and choose delete.