Select a linked PDF to view it in the Mendeley PDF viewer, where you can select and highlight text and create notes to annotate your document.

By clicking on the "Sticky Note" button in the upper left hand side of the top menu, you can add comments to your document. You can view all the notes on a document in the "Annotations" tab of the Info panel on the right hand side. You can also make additional general notes about the document in this area.

Add a "New Page" in the "Notebook" tab to make comments or save highlighted passages, and view these across all your PDFs.

By default, when you import a PDF, Mendeley does not move that file; it just creates a reference so it knows where to find that file on your computer. If you later move or delete that file, Mendeley will not be able to access it.

There are two ways to address this:

1. If you already have a folder system on your computer that you use for research documents (and you're happy with it), just move the PDF into the correct folder before importing it to Mendeley. Then, leave the PDF there.
2. Turn on automatic file organization. If turned on in Options/Preferences, this feature will move files from wherever they are imported to a designated Mendeley directory on your hard drive. You can choose if the files are automatically placed in subfolders (based on such characteristics as author name) or even whether the PDFs are renamed.