In Zotero settings, you can use which Reader opens the PDFs, EPUBs, and snapshots that are attached to your items.
The reader has three panes available, viewing of which can be toggled using the icons outlined in the image.
The navigation bar on the right allows you to see the bibliographic information associated with the attachment, as well as tags, related items, and notes you have added.
Creating annotations
In the menu bar above Reader's middle pane, there is a set of commands for creating different types of annotations:
All of these options are available when viewing PDFs, only the first three are available when viewing EPUBs or snapshots.
As you use these tools to highlight, underline, etc., the annotations you create are added to the pane on the left. When you have completed your annotations, select the notes icon (
) in the right navigation bar. Click on + next to Item Notes and choose Add Item Note from Annotations. All of your annotations will be collected into a note, which you will then see attached to your item the Items pane. By default the note will be called "Annotations" along with the date and time it was created. You can open the note and edit this so the title of the note is more descriptive. This is useful when you are later searching for notes to add to a Word or Google document.
If you prefer, you can set your preferences to open PDFs in an external reader. Externally created highlights and notes show up in the Zotero PDF reader but you will see small lock icons next to the annotations. Go to File > Import Annotations. The locks will disappear and at that point you can choose Add Note From Annotations.
Each time you add a note from annotations, a new child note will be linked to your library item. Since the newly created note will include all the annotations, you can move older ones to trash.
In Microsoft Word, LibreOffice, and Google Docs, the Zotero plug-in includes an Insert Note option.
When you choose Insert Note, Zotero will prompt you to first choose a citation style. Then a list of notes will appear, which you can choose from. Here is where renaming the notes comes in handy -- if you do not do this, it could be difficult to retrieve your note from a list of notes all named "annotations."
When you select the note, the annotations in that note will be inserted into the document, along with citations to the original document. All of the annotations in the note will be added -- there is no way to select individual annotations in the note. If you want to do that, you can copy and paste the annotation from the note display in Zotero.
The Zotero reader syncs seamlessly with the Zotero iOS app, allowing you to highlight and take notes on your iPad or iPhone and then quickly pull those annotations into a note or word processor document when you're back at your computer. Files should open automatically to your current page, no matter what device you last used.
In addition to natively supporting annotations and citations, Zotero notes now fully support embedded images. You can drag in images from your computer or the web, and they’ll sync to your other devices. You can also create an “image annotation” in the PDF reader and drag it straight into a note to easily create a cited image in your document.