In the Mendeley Reference Manager desktop app, when you double-click on an item in the Center Panel of your library, the document opens under a separate tab with the document title on the tab. Clicking on Notebook will open a Righthand Sidebar Panel with three buttons. One contains the "Info" of the document including bibliographic information, tags, keywords, abstract, etc. The "Notebook" button allow you to take notes, and the "Annotations" button keeps track of any highlighting and annotations you make on the document. To highlight, use the pen icon in the upper left corner. You can choose which color to annotate with by selecting from the color dropdown menu. To annotate, use the speech bubble icon.
You are able to open multiple PDFs at once, each in their own tab.