Sites / Sections is a sophisticated way to control the layout and theming of multiple web sites and multiple sections within a web site. When a User browses to your site, the software will apply the Site settings based upon the URL that they use (www.mysite.com). Then, based upon the applicable Section, it will choose the Master Page and Theme.
When Editing a site setting, there are 11 groups: Main Settings, Look and Feel, Email Settings, Payment Settings, Order Settings, Security Settings, Behavior Settings, Customer Defaults, Search Engine Optimization, and SSL Settings.