Tweak Settings value for max_upload_size for PHP is for cPanel-based areas such as PhpMyAdmin or webmail clients. Anything internal to cPanel would be impacted.
PHP scripts on websites would be impacted by the global php.ini file at /usr/local/lib/php.ini or via the individual php.ini files if you are using suPHP on the server. The global php.ini file is edited using WHM > Server Configuration > PHP Configuration Editor area as you did mention.
I'm delineating the above details to make it clear which does which, since the file you use or area you select matters based on what you are trying to fix.