Can the primary domain admin manage sub-domain users in Spanning Backup?

Yes!  The primary domain admin has the ability to license and manage the primary domain users as well as any associated sub-domain users.  This is all done in Spanning Backup through the primary domain admin account.  

Assign licenses to both the primary domain and sub-domain users in your License Manager.  Access the License Manager by going here as the Super Admin user for your primary domain. 

Please contact support if you have any questions.