I recently have converted back to Fedora from Archlinux and until recently was uneducated about Fedora's compiz/gnome integration. I noticed that you can "Enable Desktop Effects" which enables Compiz on login but something was missing. That something was the ability to use emerald themes without the flickering of the screen (One could autostart fusion-icon but that would also flicker the screen). To properly start compiz instead of compiz-gtk (The one Gnome uses when you enable "Desktop Effects") perform the following actions:
a) Make sure "Desktop Effects" are disabled by going to System>Preferences>Desktop Effects
b) Verify that the following packages are installed by issuing this command in a terminal window:
sudo yum install ccsm emerald-themes compizconfig-backend-gconf fusion-icon-gtk emerald compiz-fusion compiz-fusion-gnome libcompizconfig compiz-gnome compiz-bcop compiz compizconfig-python compiz-fusion-extras compiz-fusion-extras-gnome
c) From a terminal window logged in as a regular user run: fusion-icon
d) Locate the fusion-icon shortcut located in the system tray, right click on it, select "Emerald" as the "Window Decorator"
e) Create and edit compiz.desktop in /usr/share/applications/ as root
sudo gedit /usr/share/applications/compiz.desktop
f) Paste the following code into the new .desktop file and save it:
g) Tell Gnome what the default window manager should be by entering the following command in a terminal window (Logged in as a regular user):
gconftool-2 --set -t string /desktop/gnome/session/required_components/windowmanager compiz
h) Now logout, log back in, and enjoy your compiz-fusion desktop
1) To control your themes use the "Emerald Theme Manager" located in System>Preferences>Emerald Theme Manager
2) If performance is not quite up to par edit your compiz.desktop file with an editor of your choice and try either --indirect-rendering and/or --loose-binding for example
Exec=compiz ccp --indirect-rendering --loose-binding
Log out and log back in to apply the changes.