I know it can be done, I just don't know the details.
For example, we have a large project source tree. The source tree has a ton of frameworks, web apps and a lot of tools. Our entire build uses ant.
I know that from within Xcode I can add a WebObjects component to a framework by right clicking the file group (or whatever it's called in Xcode) and selecting New File. Or if you want to add an image you right click the Web Server Resource and select Add Existing Files...
Each folder in our file system is structured as:
Each one of those folders contains an ant.xml file. If you cd into one of those folders and type ant it builds that web app, framework or tool corresponding to the folder.
This is probably not much help, but that's sort of the way it works.
We also use CVS for source code control and we have developers on Mac OS X as well as Windows. Some developers use Eclipse and some developers use Xcode.
We can build from the command line or from Xcode GUI.