1. stop all services
/etc/init.d/httpd stop ; /etc/init.d/exim stop ; /etc/init.d/pure-ftpd stop ; /etc/init.d/dovecot stop ; /etc/init.d/cpanel stop ; /etc/init.d/lfd stop ; /etc/init.d/munin-node stop ; /etc/init.d/crond stop ; /etc/init.d/mysql stop ; /etc/init.d/exim stop ; /etc/init.d/portsentry stop

2. uninstall mysql, the database files are not removed, but feel free to backup them if you want
check the installed mysql packages
yum list installed | grep -i mysql
and now unsinstall them one by one, in my case:
yum remove MySQL-test.x86_64
yum remove MySQL-shared.x86_64
yum remove MySQL-server.x86_64
yum remove MySQL-devel.x86_64
yum remove MySQL-client.x86_64

3. install yum repository for percona
rpm -Uhv http://www.percona.com/downloads/percona-release/percona-release-0.0-1.x86_64.rpm

4. install percona yum install Percona-Server-client-51 Percona-Server-server-51
LATER UPDATE!!!!
please install the separate rpm from this because later you’ll run into all sort of dependency problems on centos5:
http://www.percona.com/downloads/Percona-Server-5.1/Percona-XtraDB-5.1.43-9.1/RPM/rhel5/x86_64/
you need to use rpm -ivh ~package_name.rpm~

5. now go to whm configuration section and set up mysql not to be updated automatically

6. you may need to recompile php, I needed to do it anyway so I am not sure if it wil work if you won’t compile it

7. start services again
/etc/init.d/httpd start ; /etc/init.d/exim start ; /etc/init.d/pure-ftpd start ; /etc/init.d/dovecot start ; /etc/init.d/cpanel start ; /etc/init.d/lfd start ; /etc/init.d/munin-node start ; /etc/init.d/crond start ; /etc/init.d/mysql start ; /etc/init.d/exim start ; /etc/init.d/portsentry start

8. optionally install percona xbackup
yum install xtrabackup