In preferences, you have the ability to open PDFs using the program you've designated as your System Default, or browse for another program on your computer. In Zotero 6.0 you can choose to open them with Zotero.
The PDF opens up in a tabbed interface.
In the menu that appears in the upper right-hand corner, the first option opens up the item details pane. As many articles include bibliographic information on the first page, this will assist you in verifying the metadata that was imported by Zotero.
The second option opens up a notes panel. Click on the + and choose to add a new note, which will open up the note editing window. The other option is to Add Item Note from Annotations.
In Zotero's PDF viewer, you can highlight text, select and copy an area from the document, add comments. You can also add tages to each of these types of annotation. As you create annotations, they will appear in the left pane.
If you then choose the option Add Item Note from Annotations, the highlighted text and comments are extracted and put into the notes pane.
The annotations are automatically saved. Like all Zotero library data, the annotations you create will automatically sync across all your Zotero installations. You can also create PDF annotations in group libraries.
The annotations in the notes include live links that will return you to the place in the PDF where you made the annotation. Click on the annotation and choose the "Show on Page" option.
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 annotations you will need to use this command and multiple child notes will be linked from to your library item. Since the newly created note will include all the annotations, you can move the older ones to trash.
In Microsoft Word, LibreOffice, and Google Docs, the Zotero plug-in includes an "Add Note" option.
When you choose Add Note, Zotero will prompt you to first choose a citation style. Then a list of notes will appear, which you can choose from. When a note is created from annotations the heading says Annotations (date, time). It will be easier to find the note later if you rename the heading to something more easily recognizable, like an author's name or the first few words of the title.
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 PDF 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. PDFs will 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.