Those come from a template that cPanel uses to built the virtual host. I'd look at the documentation on virtualhost includes (http://docs.cpanel.net/twiki/bin/vie..._Include_Files) You can create a configuration file that will only be picked up by that one domain. It adds the include at the very bottom of the virtualhost container. If I understand LSWS correct it will pick up the last version of the directive (i.e. if there are multiple open_basedir) so the includes 'should' work perfect with LSWS.