How can I use the mult-domain plugin to administrate all my urls on the same server?

I have a seo server that has a lot of domain names, url's. I am trying to get a setup where I can perform basic admin task all at the same time. I installed the multi-domain plugin and I have added several urls but Im not sure what to do next. All of the urls have a existing wordpress install, is that an issue I need to fix? I have followed the steps on the multi-domain page but I really dont know what Im doing. Just to wrap up-I have one server, lots of urls that currently have their own wordpress install. I am wanting to do a multi-domain setup to administrate all of them. How do I do it?