When working with EndNote, it is best practice to only ever have one EndNote library. This is because if you need to sync your library or merge documents later down the line, having multiple libraries will confuse the program. Instead of having multiple libraries, you can use Groups and Group Sets to organise your EndNote Library.
You can arrange your references in the ways that work best for you. You can store and manage your sources in Standard and Smart Groups, and these can be arranged as Group Sets.