A native PHP version is a version from the official repository of an operating system. You can set up alternative PHP versions from the ISPsystem repository. To do so, go to Web-server settings → PHP setup and click Install.
PHP versions are installed into /opt/.
In Web-server settings → PHP you can see the versions for every PHP mode.
PHP versions for subdomains will be automatically inherited from the main domain if you have enabled the option Auto subdomains when creating the domain.
Log in to the control panel as Admin, select the PHP version and click Apache module to apply it to all the WWW-domains of the ISPmanager users with the mode "PHP as Apache".
For FastCGI (Nginx + PHP-FPM) the version can be changed in PHP list at the user level or in the user editing from at the admin level. Changes apply to all user's WWW domains using PHP in FastCGI (Nginx + PHP-FPM) mode. This way, the setting is applied to the user.
Learn more under PHP modes.