You can take notes on sources within Zotero and for PDFs, you can annotate and write notes directly in the document. You can copy and paste those notes into your documents, or export them to print or save elsewhere.
Click on a source (either from My Library or a specific Collection) that you want to take notes on
Click on the Notes tab in the right panel
Click on Add to start writing a note
In the note screen, a top menu bar has icon options to format the text, choose a text color, highlight note text, and insert a link
At the bottom of the note screen are options to relate the note to other notes and sources and/or to tag the note
In the library you are working from, right click on the source you have added notes to
Select "Generate Report from Item"
Zotero will create a report with basic citation information, tags, notes, and, if existing, a URL
To print or save the report, click on File in the report's top menu bar and choose accordingly
Click on a source (either from My Library or a specific Collection) that you want to take notes on
Double-click on the PDF title - will open in another window (see green box in the image below)
In the top menu bar, there are icon options to highlight text, add a note, and select an area of text which will create a box around the text area (see red box in the image below)
The notes will automatically add a page number and there is also a place to add tags to the note
After marking up text and taking notes (see green box in the image below), go the right panel section
Under "Item Notes," click on the + sign, and select "Add Item Note from Annotations" (see red box in the image below) - this will populate the notes field (see purple box in the image below)
Note: you can return to the PDF document any time and make more notes, though you will have to also repeat step 6 to upload your new notes.
Close the PDF reader to return to the Library you were working from
You will notice an "Annotations" line next to a sticky note icon (see red box in the image below) under the title of the source you were notating (see green box in the image below)
To get only your notes, right click on "Annotations" and select "Export Note" (see yellow box in the image below)
To get notes plus the source title, right click on "Annotations" and select "Generate Report from Item" (see purple box in the image below)
The report layout will look like this:
To get notes plus full source description information, right click on the "Source Title" (see green box in image below) and select "Generate Report from Item"
The report layout will look like this:
To print or save the report, click on File in the report's top menu bar and choose accordingly