Zotero has an integrated PDF/EPUB reader that allows to highlight and annotate documents saved in your Zotero library. While in Zotero, double-click to open a document.
The buttons for marking up a document are, in order:
Below are examples of how some of these functions look on a document in the reader. "Draw" is free-form and works especially well with a stylus. "Text" lets you type comments directly onto the page.
In practice, highlighting may not always work due to the formatting of the PDF. If the PDF was born digital or was scanned from print using OCR, then highlighting will work, but if it was scanned from print without text recognition, highlighting won't work.
Notes look like sticky notes on the page, but only show the note text when clicked. Like the Notes that you attach to the citation, text in the reader's sticky notes is fully searchable.
"Select area" encloses an area of the page in a box; use this option if your PDF cannot be highlighted.
You may pick from five colors for the highlighting, notes, and lines.
Use the panel at the left of your reader document to display all your notes and highlights.