To install or upgrade cse simply do the following from the root shell via SSH:

rm -fv cse.tgz
wget http://www.configserver.com/free/cse.tgz
tar -xzf cse.tgz
cd cse
sh install.sh
cd ..
rm -Rfv cse/ cse.tgz

Then login to WHM and scroll to the bottom of the left hand menu and you should see "ConfigServer Explorer"


If you want to uninstall, simply:

rm -fv /usr/local/cpanel/whostmgr/docroot/cgi/addon_cse.cgi
rm -fv /usr/local/cpanel/whostmgr/docroot/cgi/cseversion.txt