ProSites Best Practice

I'm new to setting up a blogging network, but am keen to use ProSites to help me monetize. If I understand it correctly, ProSites is for each member that wants to maintain a site on the network, they can, for example in the Freemium Model, get one for free, and pay an upgrade for premium plugins, I suppose. All of the blogs could be collected on a central location, and I suspect should be marked as no index, no follow. I wonder, though, what happens when I use the domain mapping plugin and someone on the network has their own URL rather than a subdomain of the network URL. Will this blog still be collected on the central location?