The VPN3000 will simply pass off the users credentials to the configured NT server. It is up to the trust relationships within your NT domain and the permissions of that NT server as to whether you can authenticate users in other domains.
For a start the NT server you configure should be a domain controller, and the domain that it is a part of should have a trust relationship (one or two-way) with all the other domains that you want to authenticate users from.
There is nothing specific you can do on the VPN3000 to do what you want to do, it is all done on the NT network.