Using php-fcgi is realy easy in ispconfig, you just have to select it in the website settings. Go to the website settings, select "php-fcgi" in the php settings and enable the "suexec" checkbox. Then click on save and wait a minute to get the changes applied.
If you get any errors with your php application, then you most likely uploaded the files with a wrong user, e.g. root. You have to chown all files to the website user and client group then. For details see error.log of the website.