I have used fedora 12 in the past with fusion-icon+compiz+emerald. I had no issues using those apps together. I did, however, install via YUM. So, I would like to help you out; however, if your against using yum i wouldnt be able to. I just have not used rpm enough. You willing to try installing the packages from rpmfusion via yum? if so, try :
su -c 'rpm -Uvh http://download1.rpmfusion.org/free/fedora/rpmfusion-free-release-stable.noarch.rpm http://download1.rpmfusion.org/nonfree/fedora/rpmfusion-nonfree-release-stable.noarch.rpm;yum remove compiz'
then allow the install to rebuild your conf file with by clearing the old one out
run this as user not root)
rm -rf ~/.gconf/apps/compiz
then get all the new compiz stuff:
su -c 'yum install compiz-fusion compiz-fusion-gnome compiz-fusion-extras compiz-fusion-extras-gnome compiz-manager gnome-compiz-manager ccsm fusion-icon fusion-icon-gtk emerald emerald-themes'
I did it this way on 4-5 fedora installs with no issues. If you would like to see what i used as refs check out fedoraunity.org
( great howto for fedora by the way)