It is possible to create separate folders for different projects or texts.
Click on Collections -> New Collection in Mendeley Reference Manager.
Pull a reference from All references to a chosen folder or from one folder to another.
You can also select the reference (check the box next to it) and click on Organize in the toolbar down below and then Add to collection. You may select more than one folder to add the reference to.
Your references can be found in All references even if you add them to other folders.
Create a subfolder by right-clicking on a folder and then New Collection.
You can add notes (notebook), comments (annotations) and highligts (highlights), to the documents in your Mendeley library.
You can share your references and documents with other people by creating groups in Mendeley: