To make annotations on PDF documents, you can use the ChromeBook built-in annotation tool.
Steps
Download the save the PDF document
Open up the PDF document from your File Manager
The PDF document will open up on Chrome. At the top bar, you will see a pencil symbol. Click on it to start annotating.
To save the file, click on the 'Print' icon. From the drop-down list, click 'Save as PDF'.
You can view the YouTube video below: