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There are many different ways to organize your RefWorks library. Most of which can be done on the left side of the screen through the menu.
The two primary ways of organization are with folders and tags.
Folders can be a great way to consolidate specific references into particular places. For this example, it has topics such as Hetch Hetchy and Music listed. It also has a database (PubMed) listed as well. Other examples could be for specific classes, topics, places, etc.
Tags are also important when organizing your RefWorks library. Tags are essentially keywords that are connected to a particular reference. This is a list of some of the tags in my RefWorks.
The other place tags are and where you can add additional tags are in the individual reference in edit mode. Edit mode can be found if you click on the pencil 
in the upper right corner of the page when an individual reference is selected. With tags, they can narrow down specific keywords relating to the topic of the reference and if you have multiple references with the same tags, they will be grouped accordingly when you click on a tag.