If you try and do a discovery of these domains and servers does it find them? - No data is uploaded to the data warehouse until you configure the data synchronisation job - so you can delete the servers or domains if you need to.
I have found that name resolution can be a problem in an AD environment and the things to look at is DNS reverse lookup zones configured correctly. But since you have manually imported the servers it looks like you are having issues with the account that should access the servers to get WMI. Registry and perfmon data.
Is the computer on which the data collector installed a member of the domain?
Have all firewalls been diabled on the data collector.
Can you acces the registry and perfmon counters remotely - from the data collector server?
Is the account you are using to collect inventory and performance data a memeber of local admins group on all the servers?, Are all the servers in the same domain - if any are in a workgroup then you need to us a local computer account with local admin rights to the computer.
Are any of these servers behind a firewall - you will need to deploy an additional data collector in the DMZ, as you will have very little chance of convincing the firewall administrator to allow the required ports to be opened.
Is the data collector server a windows 2003 server - see the CP documentation for things you need to consider when using 2003.
