Can I use WP Empire Builder to manage existing blogs?

The whole idea of Wordpress Multisite is to create a network of blogs that share the same Wordpress database. If you have already set up a blog before, then it means that that partictular blog has a Wordpress database of its own and can't be a part of the "network."

That said, you can still set up a new child blog in your network and then import the content of your previous "stand-alone" blog in that new "child blog." You can only import the content (not the plugins or themes). You can find instructions to do this here.