>When installing WWC so far, it was only for one domain. So, when it prompts, at first, to select the domain, I was always entering the domain for it. Now, one server serves two domains. How can I achieve that to have a setup for both domains without having to run WWC setup twice?

Did you ever figure this one out? I have 2 domains running on the same Win2k Server. All I really did was run the Console under the Web Connect menu and ran the Configure Server option. I also had to run the IIS Manager to set up some stuff as well, but you would have done the same steps with that in setting up your first domain.