Regarding you might recognize your files on your web contructed by your PHP-scripts are grouped as NOBODY you can avoid this problem by setting up an FTP-Connection ("ftp_connect", "ftp_raw", etc.) and use methods like "ftp_fput" to create these [instead of giving out rights so you can use the usual "unsecure" way]. This will give the files created not the GROUP NOBODY - it will give out the GROUP your FTP-Connection via your FTP-Program uses, too.
Furthermore you might want to hash the password for the FTP-Connection - then check out:
http://dev.mysql.com/doc/mysql/en/Password_hashing.html