Does StackExchange 2.0 sites share the same code base with SO, and thus, are automatically update when SO is updated? Or is a fork of current SO code?
The original Stack Exchange was a fork of the Stack Overflow code base, this led the unfortunate effect that lots of bugs and features were introduced and fixed in the main SO site but not rolled out to the Stack Exchange sites.
Stack Exchange 2.0 runs the same source so all the fancy new features that become available on Stack Overflow will become available on the Stack Sites.
One exception is the Area 51 site, it runs a custom fork of SO (for obvious reasons) and another bit to keep in mind is that we will often stagger releases (and quite often meta is the first place new features manifest)
From this blog post:
Q: Is there a difference between the Stack Exchange code base and the Stack Overflow code base?
The Stack Exchange and Stack Overflow sites run on separate, but very similar, versions of the original software. When Stack Exchange started, they forked a copy of Stack Overflow, then each team continued to develop and improve their respective platforms in separate development efforts.
Currently, the combined Stack Exchange and Stack Overflow teams are in the process of merging the two code bases to take advantage of the best features of the two systems. Sites created under the Stack Exchange 2.0 model will take advantage of the new code base, as will Stack Overflow, Server Fault, and Super User.
Though it doesn't fully answer for the future.
I think you are looking at it backwards.
Stack Overflow is running on the Stack Exchange platform. So, Stack Overflow, Super User, Server Fault, Meta, WebApps, and Meta Web Apps are all running on the same software.