Re-Naming Files
File name conventions differ for documents you download from the Internet. Some names may just be a series of numbers. Mendeley allows you to easily rename those files to aid consistency, identification and organization.
In Mendeley Desktop, select the document(s) you want to rename, and pull down the File tab and select Rename Document Files..
You get to choose the name convention by dragging fields to the position you want.
Organizing Files on Your Computer
You can also rename multiple files using the File Organizer. It also can sort your files neatly into a designated folder and sub-folders on your computer's hard drive. To access the File Organizer:
Mac: Mendeley Desktop>Preferences
Windows: Tools> Options
Once you've added references, you'll probably want to organize them, so that you can easily find and identify documents. Open Mendeley Desktop and see how all your references are listed in the center pane.
Sorting by Reference Headings
Each references is organized into fields - Starred favorites, Read (grey)/Unread (green) button, Type of Document indicator (.pdf, MS Word, etc.), Authors, Title, Year, Publication and Date Added to Mendeley. If you click on any of these headers, your list of documents will be sorted accordingly.
Creating Folders
The right pane offers other organizational categories, including folders. Folders allow you to easily distinguish documents by subject, paper or any other category. References can be put in more than one folder. Just click on Create Folder to add new options.
Using Filters
Another way to sort your references is by using filters. If you look at the left pane of both Mendeley Desktop and Mendeley Web, you'll see a filtering feature. (If you don't see it on the desktop version, click the small funnel symbol in the lower left corner.) You can filter your documents by Publication name, Author's keywords or the tags you've added to a document's record.
For more information about adding citations to papers, watch the MENDELEY VIDEO TUTORIAL: ORGANIZING YOUR LIBRARY
http://www.youtube.com/watch?feature=player_embedded&v=VD1z0boSpQY