You can use both the external LDAP/AD or the Cloudron user management. Users synced from LDAP will be marked accordingly in the Cloudron dashboard.
Cloudron also can handle as many domains as you like, however the dashboard is only installed on one. So all users logging into that dashboard would have to use the same domain. From what I understand your case, it may be better to just create individual Cloudron instances per organization, then all this is probably easier to manage.