Fedora Core on linuxquestions.org
Linux Home Server How-To (Fedora Core 5 specific)
To get compiz to start with your selected emerald theme automatically, as root edit /usr/bin/compiz-manager and locate the lines:
# Don't use emerald by default (to avoid additional requirements)
USE_EMERALD=${USE_EMERALD:-no}
Change it to read:
USE_EMERALD=${USE_EMERALD:-yes}