Louis Polycarpou has written a blog entry to explain an important point about JavaCAPS 6 and Glassfish configuration of additional domains.
CAPS 5.1.x users will notice that there is no longer a domain manager tool to simplify domain management tasks such as domain creation. This was effectively tied to the Sun SeeBeyond Integration Server, which no longer exists, but the domain manager may return in future releases.
Read the full article.
On my side I hope Sun is going to make this procedure simpler, as it was with version 5. The suite is already big and complex enough, we do not really need to remove tools which make our life easier.