The following guide will show you how to enable Ioncube for cPanel.
Login to WHM as the 'root' user.
Navigate to "Home » Server Configuration » Tweak Settings."
Click on the "PHP" tab.
Select the "ioncube" option for "cPanel PHP loader."
Click the "Save" button.
Please note that this only enables Ioncube for cPanel/WHM/Webmail. It doesn't enable Ioncube for Apache's PHP versions. Ioncube is enabled for Apache's PHP versions by installing the Ioncube PHP extension through EasyApache.