The Permission Matrix contains different tabs for different parts to the system and for different system items. On each tab every action/property is listed. Use the table to set permissions for operations such as viewing, editing, creating... and so on. You can give different permissions to different scopes of the system (System, Organization, Group, User).
Tabs Configuration, Agent Menu, Special Permissions and Entity Actions are used to define access permission to system menus and function permissions to forms and views, etc.