Mendeley automatically sorts your references into the categories Recently Added and Recently Read. You can organize your library by creating collections for different projects or subjects. They work a lot like folders. To create a collection, click on New Collection under Collections in the menu on the left. If you want to create subcollections to a collection you can right click on it and select New Collection. When you have created a collection you can drag and drop any references you want to add to it. All references will always remain under All references, even if you add them to one or more collections.
Another way to organize your references is using tags. You can select a reference in your library and add one or more tags to it in the Tags field, under the Info tab.
You can then filter for all references with a given tag using the filtering function next to the search field. Click on Tags and choose the tag you want to search for.
Alternatively, you can search for it in the search field, but this also generates results from other metadata fields, such as words occuring in titles or abstracts.
You can open an added PDF file in Mendeley's built-in PDF reader by selecting a reference and clicking on Read under the Info tab. In the PDF reader you can read, search through the text and add highlights or notes.
Any notes you add will be visible under the Notes tab for the specific reference in the main Mendeley window.
(This section is a work in progress. For more information on this function, see Mendeley Support Center.)