Zotero's inbuilt PDF reader allows you to highlight or annotate text or images and extract these as notes. To do this, follow the instructions outlined below.
You can separate your comments from your selections by changing the colour of the pen. This makes it easier for you to see, at a glance, whether, you have a task e.g. 'look up the book in the library' or are highlighting a quote. You can also use colours to code your documents.