I am fighting with Xcode 4 workspaces. Currently Xcode 4 wins. Thus, my situation:
I have the workspace with the iOS app project. There is also static library project iO
I was not real happy with any of the other solutions that were provided, so I found another solution that I prefer. Rather than having to use relevant paths to put the /usr/local/include folder outside of the installation directory, I added a pre-action to the Archive step in my scheme. In the pre-action I provided a script that removed the usr directory prior to archiving.
rm -r "$OBJROOT/ArchiveIntermediates/MyAppName/InstallationBuildProductsLocation/usr"
This removes the usr directory before archiving so that it does not end up in the bundle and cause Xcode to think it has multiple modules.