As of July 2013, PHP Selector support for ISPmanager is limited to command line utilities. You should still be able to use it.
As always, PHP Selector requires CGI, FCGI or suPHP to work.
You will need to do following modifications:
Create new file /usr/local/bin/php-cgi-etc
/usr/bin/php-cgi -c /etc/php.ini "$@"
Make that file executable:
$ chmod +x /usr/local/bin/php-cgi-etc
Edit file /usr/local/ispmgr/etc/ispmgr.conf
path phpcgibinary /usr/local/bin/php-cgi-etc
Make sure there is no other lines with path phpcgibinary defined in the file.
$ killall ispmgr
After that FCGID wrappers (/var/www/[USER]/data/php-bin/php) for new users will be like this:
You might need to edit/modify wrappers for existing users if you want them to be able to use PHP Selector. You can leave them as is for users that don't need such functionality.