When you create a new maintenance organization you need to assign it to an appropriate Site. The site is connected to a company and thus, when establishing new employees and connecting them to a maintenance organizations, the employee will be connected to the company, through the maintenance organization and site.
Site is also used when creating object identities to define who owns, or who is responsible, for a certain object or object structure. A work order will be created for the site to which the object identity belongs.
Sales parts, inventory parts and purchase parts are also entered for a specific site, and consequently customer orders, purchase orders and inventory is always 'owned' by the site.
A company is a financial entity, and to a company you can connect one or several sites. The Site is the 'owner' of objects, work orders, customer orders, inventory parts etc. To one site you can connect one or several maintenance organizations, the maintenance organization being the 'owner' of the personnel resources (employees).