I have a small suggestion to the developers of this plugin. Perhaps it would be useful, and clear up some confusion, to add a note to the plugin description that WordPress must be installed in the root of the public web path in order to map domains. There's a lot of info on that page but folks really only need to read that if they pass the prerequisite of having WP installed at the right location.
This is also a very common question in the Multisite Forums. Stuff like:
"How can setup my multisite installation with several domains?"
--> "Do you have multisite installed in /public_html?
"No it's installed in /wp/
--> "Then you can't map domains, at least not with this plugin."