Sites are the main driving force of the system. They are essentially larger pools of items and apps that are segregated and only meet in cross-sites applications. Think of sites as your house, your shed, or your car. When designing a site think about who has access and who will be using it the most often, what permissions might be needed, and do you need all the apps active on the site. The more sites you have the more bloated the system can become so beware making tons of sites. Thats why Zones and Locations exist.