With Mendeley you can annotate PDFs by adding highlights & text notes in the PDF.
In the Desktop:
You can also keep general notes about the entire article to the right of the PDF view
Keep track of useful or important resources by favoriting them. Just click the star next to the PDF icon.
You can see all your favorites at once by clicking the Favorites option in your library.
There are two ways to create folders in Mendeley Desktop. You can click on the Create Folder option at the bottom of your library or you can click on the icon at the top of the Desktop component.
Add a subfolder:
Create a Folder in Mendeley Online: