Zotero has a built-in PDF, EPUB and snapshots reader that allows users to open files in a new tab, easily navigate between them and the library, highlight, annotate them, add comments or tags to the highlighted parts and annotations, and extract the annotations into a note. Links in the annotations allow users to quickly find the location of the highlighted sentence or note in the PDF or EPUB document.
Annotations are stored in Zotero itself, not in the file. They do not appear when the file is opened in an external reader. This makes it easier to synchronise annotations for PDFs shared within a group. However, it is possible to export a copy of the PDF with the annotations embedded (File -> Export PDF from the Library view or "Save As" from the PDF reader) and continue working on it outside of Zotero.
PDF annotations added in an external PDF reader will appear read-only in the Zotero PDF reader, but can be imported into Zotero by selecting File -> "Import Annotations..." from within the PDF reader, where they will be fully editable.
You can split the reader horizontally or vertically (right-click or View menu ). For example, it may be useful to have the text on one side and the endnotes on the other side.
