If you have used the Build Server inside Visual Studio Team System, you must have notices that after you create a new Build Configuration you cannot change the TeamBuild.proj file.
The Build Server creates a folder inside the Source Control with the name of "TeamBuildConfigurations". you can notice that you can not check out the file for edit and if you try to edit it, it is not checked out.
The reason for this is that the folder TeamBuildConfigurations is not mapped in your Workspace, which means the Version Control doesn't know where to check out the files. I would expect it to popop a window and ask me but then again this is a beta.
Workaround: You need to map the TeamBuildConfigurations to local folder. Go to File -> Source Control -> WorkSpaces... -> Choose a workspace and press Edit. On the table at the bottom you need to fill on the left column with the Source Fontrol path to TeamBuildConfigurations. On the right column you need to map it to a local folder. Then go back to the Source Control view and refresh.
Now you can check out the file and edit it.