If you need to change your php handler, you’ll need to do so from the WHM.
Once you are on the Configure PHP and suEXEC option page you can change your php handler. On my account I can switch between suPHP, cgi, and fcgi. I like to use fcgi as it decreases the server load on the cpu more that suPHP does.
Once you have the handler you want to use go ahead and Save New Configuration.
Here is some documentation comparing the different handlers: