Primary sites are used to specify connections to SCCM infrastructures or modify existing entries. Additional information can be found here.
EM and SCCM distribution points are listed in the "Distribution Points" section. They are created automatically once a primary site has been set up and communications with the EM server are established and can be synchronized via the "Synchronize SCCM Distribution Points" button. Click one of the distribution points to modify certain settings of the respective distribution point (see following screenshot).
The EM Distribution Point service (M42EmDp) must be restarted after modifying any settings.
The "Settings" menu is used to configure actions that are created in the EM and the SCCM. For instance, you can specify the folder where new collections in SCCM shall be created.