On her blog today Nessa has written up a tutorial on getting SuPHP working along with cPanel on your system.
I wrote this tutorial a while back and figured it would be good to post because suPHP is growing more popular as an alternative to phpSuExec. The instructions assume that you are on a Linux cPanel server and are familiar with how to install PHP, but do not want to use EasyApache’s suPHP installer in WHM.
It's a long process but a lot of it is just configuration changes and grabbing the right software. Every line of each of the config files you'll need to change is there ready to cut and paste into your files as well as the command line calls you'll need to make to configure/compile and move files to where they need to go.