You could add the entries to /usr/local/apache/conf/php.conf file, which contains the other FCGI directives. If you edit this file, you'll have to ensure the file is not replaced during EasyApache update. You could use a script at /scripts/posteasyapache to simply replace any copy cPanel adds with your own version.
Please note that any time you run either /usr/local/cpanel/bin/rebuild_phpconf or WHM > Apache Configuration > PHP and SuExec Configuration area, you'll be replacing php.conf file with the cPanel version
For adding entries for FCGI, you'd be better off adding them to /usr/local/apache/conf/includes/post_virtualhost_global.conf file for adding those entries instead of directly editing php.conf file as was suggested.
After you have added any entries for FCGI into post_virtualhost_global.conf, simply restart Apache for the new settings to take effect.