To take notes on a piece of content, make sure that the file is open and that you are in the secure reader. Once inside, look for the icon tools in the upper right-hand corner. If you hover your cursor over each one, a popup will appear, telling you what the tool does.
After selecting a tool, you will need to select the location in the document where you would like to use it, by clicking on that part of the screen. To view more tools, use the down arrow icon, which will extend the toolbar.