If organization has two domain names abc.com and xyz.com, then you need to import the users from both the domains by having separate active directory user import profile in SapphireIMS. If the username say testuser belongs to abc.domain.com then either he/she has to login to SapphireIMS portal using username: abc/testuser along with the password OR he/she can login using username: testuser@abc.com along with the password.
Integrated Windows Authentication can be achieved using 2-way AD trust.