You can choose which space to store content. All your data goes under company home. If you want to store it in a share site then it goes in under company home/sites/sitename/. If not then it goes somewhere else of your choosing.
Alfresco Share is a user interface, that's the "important function"
You can put content into Share sites in which case they will have the collaboration features associated with sites in share such as Sharepoint protocol, Bogs, wiki, document library, site management, site invitation etc.
Or you can store content in other spaces, with their own content models, security and functionality.