yahavatar
m34,
New here, but there are several solutions that I can think of. I'm guessing what you really want to know is how to share content/plugin/template files between two sites?
If so, you can just move those directories to a directory level above the root directory of the sites. Then, create symbolic/hard links to those directories from each of the sites. Then, it's a matter of configuring one of the sites to not have a header/footer.
This works for me. I am currently doing it on a Windows 2008 server, but I could just as easily have done so on a *nix box.
If you'd like a more detailed explanation, I'd be happy to give one.
yah.