In some light-weight scripting that I have done, doing an LDAP bind to 3268 allowed me to access AD records in different domains. I tried modifying the port but it still does not work properly. It will allow me to point to a domain controller in domain "A" but use admin credentials and domain name from domain "B", but it will not let users from both domain "A" and domain "B" login at the same time. It does not matter if the username includes a domain or not, it seems to always want to use the domain name specified in the Import Users page. If that domain name matches to the user's domain, it allows them to login, if it does not it tells me the password is incorrect.
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Currently Alert Central really only supports a single domain. We have multiple domain support on the roadmap.
Check out the Feature Requests for AC link below for multiple domain support. If you don't find one already listed then create a feature request for it.