I have never done an upgrade of MySQL from rpms before. I currently run 5.5.19 and just want to bump it up to 5.5.20. I am running the Generic Linux RPMs from here: http://dev.mysql.com/downloads/mysql/
Take a backup of your databases just in case something goes wrong (we never know). Then upgrade the RPMs via yum/up2date, or just use the rpm method you used before. I don't know if YUM would work on a custom-built MySQL via RPM, so just upgrade as you would like before.