You can install MySQL in a different location, either by using the binary
or source distribution from MySQL. As the Cpanel uses the RPM install and
installs MySQL in the default location, /var/lib/mysql.
We did this on our server as we run two differnet MySQL server/clients
for production and development projects. We removed the RPM version and
had to make various modification to the Cpanel skins.
After removing the RPM MySQL version, (rpm -e MySQL),.. we had to create
a symbolic link from the /tmp/mysql.sock to /var/lib/mysql/mysql.sock.
Or if you want to leave the MySQL installed for the Cpanel. Then simply
install a second copy, using a differnet socket and TCP/IP configuration
and setup and config a my.cnf file in the new MySQL base directory.
I recommend building from the source distro, alot more flexibility.
Hope this helps.