I actually put a whole whack of multimedia tutorials for WebSphere Application Server together to try and address the real lack of documentation on the topic.
Here's a seriously cool tutorial that covers just about every aspect of deploying an ear file to WebSphere, including the setting up of connection pools, message queues, resource references and the like.
I think it's an earlier version, but the screens really haven't changed too much from one version to the other.
I think you'll find all of these free tutorials, including ones on development with IRAD, very helpful. Share the link with your friends.