An EndNote library is your database of references, including any file attachments.
When you create a new library the system automatically generates a second folder with the same name. The second folder is a data folder. They are the .enl file and .data file. Both these folders must stay together and if you chose to move one folder the other must be moved to the same location. Deleting any one folder will corrupt your EndNote Library.
You can have multiple EndNote libraries. It is better to have one library, organized into Groups.
Note: If you plan to sync your library with Endnote web you will only be able to do this with a single library on your desktop.