Configuration files:
/usr/local/etc/suphp.conf (Detailed suPHP configuration)
/usr/local/apache/conf.d/suphp.conf (suPHP configuration for Apache)

There is also suphp configuration in the vhost files for each vhost.
/usr/local/apache/conf.d/vhosts/DOMAIN.COM.conf
/usr/local/apache/conf.d/vhosts/DOMAIN.COM.ssl.conf

If you don't want to allow users to modify and use custom php.ini per folder you can do that by placing an empty php.ini file into users home folder. The empty file will use default server php.ini and will not allow users to load any custom changes and other php.ini files.

Example:

touch /home/USERNAME/php.ini

Now secure it so users can't change/disable it

chown root.root /home/USERNAME/php.ini
chmod 555 /home/USERNAME/php.ini

Default php.ini
/usr/local/php/php.ini

Note that each version of PHP in PHP selector has a different php.ini file.
You can edit php.ini files for each version from the php selector in cwp.admin