In rare instances when you do an Archive and Install your save user and network settings may be grayed out. It still is OK to Archive and Install, you will just find your user folders end up getting moved to the Previous System Folder along with the old System folder. If after having done an Archive and Install your iTunes music library, iMovie projects, or iPhoto library are gone, they have simply been moved to the Previous System folder in the Users's Music, Movie, or Pictures folder respectively. Quit your iApps and move the documents to their corresponding location on the hard drive's Users -> yourusername -> Music, Movie, and Pictures folder, and that should restore your documents to where they were in the past when you next reopen the iApps.
Note to AOL users, the Shared folder contains important documents and should be restored with its documents after an Archive and Install is performed regardless of whether or not you were able to preserve user and network settings.