Will the Super User, Stack Overflow and Server Fault sites be put under the umbrella of the new Stack Exchange 2.0? Or will they stay separate?
The combined Stack Exchange/Stack Overflow teams are integrating the best from both platforms into a new, faster, more versatile platform (Stack Exchange 2.0). While, technically, the trilogy sites will be running along with the "Stack Exchange 2.0" larger community of sites, they will almost certainly be running their own "special version" of software for the foreseeable future. There's just too many performance optimizations specific to those sites to just switch platforms mid-stream. But the new sites will be created under the new platform.
There's also the issue of how the new communities will be created. The trilogy sites already have well-defined communities so, obviously, they will not need the "Site Proposal/Commitment" process to form viable communities.
But there are lots of cool infrastructure changes in the works (like API work, etc) that will bring many cool, new capabilities to all the sites, SO/SF/SU included.
I can see no foreseeable reason why StackOverflow and StackExchange must interact at all, or be part of the same umbrella.
While it does say that the two code bases are being merged, and most like StackOverflow and the other 2 will help to promote the new StackExchange sites, I highly doubt that any huge changes will be coming to StackOverflow because of StackExchange.