A site is for the most part a geographic spot belonging to your company where your company conducts business. Units and rounds needs to always be assigned to a site. Depending on how you want to manage your company's sites, they do not have to be geographical spots, they could just as well be something else entirely. Look at it as a parent or placeholder for your units and rounds.
A very useful feature with a site is that you can easily filter out deviations, expenditure etc. on several units or rounds assigned to that specific site. It is also the site that is the key component when assigning permissions to users.
You can also apply sections to a site and there are no restrictions as to how many sections you create under each site. You can easily create a section under your site by clicking on the Sections-tab and then clicking on the Create a new one here!-link. When a section is created you can then attach units and rounds to a specific section. It is also possible to limit permissions on a user basis for each section.