When it comes to themes in Frameworkbuilder you can think of templates. With a template you can easily share common design areas of a site without having to manually keep track of each place where that design is displayed. You can just update the template file to force all of the other pages derived from it to be updated in DW.
Themes work kinda like this but are much more robust. Rather than having the common elements of the page come from a template file you can use Framework builder to use include files for the common elements. This allows you to make changes to the pages that make use of this include by updating the include file only. There is no need to reapply anything to the pages since they have the includes on them. This is a great way to offer quick and easy updating of the design elements as well as have the potential to have many different themes in use and have the active one selected using parameters to completely change the look and feel of your site. You can also use parameters to include or exclude portions of the page for greater flexibility. Here is a link to the getting started guide, it explains how to make use of the themes and plug-ins: