Re: Registering New Users to a specific blog (subfolder)
Your users have to register with wpmu and that means the main blog initially. If all you want is for them to be registered users in your community blog automatically then try this plugin: http://code.ourcommoninterest.org/2009/01/02/community-and-group-blogs-in-a-can/
Activate and configure that plugin on your community blog and when your users visit the blog for the first time they will become registered users at whatever level you set in the admin screen for the plugin.
I think that is what you want.