The core application will be identical between CE and PE, which implies that all extra functionality that PE will have will be in the form of extensions. From this it follows that both CE and PE will have the capability to run multiple portals, however, PE could contain enhanced portal management modules to make it easier to manage a large number of portals.

Also, it is very important to understand that PE will build on top of CE, not the otherway around. Future versions of CE will not have less functionality than current CE versions, simply because that would mean breaking changes.

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http://www.dotnetnuke.com/Community/Blogs/tabid/825/EntryId/2225/DotNetNuke-Business-Model-and-Product-Roadmap-Part-1-of-2.aspx