WHM/cPanel Gurus, need some assistance please.

I am not a WHM/cPanel person, I prefer a more direct approach to maintaining a server.  However, I understand that if one is going to be reselling space on a server that WHM/cPanel can make that easier so that clients don't/can't screw with server settings.

I am trying to change the mySQL server configuration but can not find where to do so.  I installed ConfigServer Explorer on WHM to make it easier for me to navigate the server but I am still unsure where to configure mySQL Server.  I don't understand, or I don't know where, MySQL configuration is done through WHM; I see where I can change configuration for Apache and PHP and other areas so why isn't there something for mySQL?  Or if there is, where is it?  Searches on the internet have not been helpful.

cnf file ....

You can edit the /etc/my.cnf and restart mysql. No need to mess around whm.

OK, so did a little reading on how to determine which config files are read, issued the command and got:

Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf /usr/etc/my.cnf ~/.my.cnf

So are they all read in that order with configurations applied in an hierarchy?

The /etc/my.cnf has:

[mysqld]
innodb_file_per_table=1
open_files_limit=4534

and nothing else.

On my server I installed the mySQL server and did some preliminary configuration through the shell.  I then installed webmin which gives me a GUI to the mySQL configuration as well as access to the config files.  I find that really easy to work with.