Yes, you can definitely have multiple domains as long as their is a trust relationship. You can set up multiple organization units. Then when you add application users, it will validate that they exist in one of the saved organizational units.

For example, let's say you hook up LDAP://DC=ABC,DC=com and LDAP://DC=DEF,DC=blackbaud,DC=com and add users from both domains into your local instance. As long as you can use the LDAP protocol and have a user/password that can connect to it.