My organization is splitting from another organization but we need to keep email access on the old organizations exchange server until our new servers are setup. There is not a trust relationship setup between the domains. We have this working in a test environment using Outlook Anywhere, but we would like to be able to configure the entire department this way without having to manually change the account settings on every computer. Is there a way to automate this configuration? I tried setting up Autocdiscover in DNS but it seemed to get caught up in the way we have DNS setup(example.com is our website that is externally hosted, department.example.com is our internal domain. Autodescover seems to hit the external site. Not my idea.). Any help would be greatly appreciated. Thanks in advance.

If your new organization is separate AD forest (and by that also separate Exchange organization) then answer is no - you can't automatically reconfigure your clients since they will actually be accessing completely new system.