All I've had to do is make sure the ownerships are correct, and that nothing is world write-able. I used the following commands in terminal to fix sites when I switched from DSO to suphp. (change user for the actual username of course).
Code:
chown -R user:user /home/user/public_html/* ;
find /home/user/public_html/ -type d -exec chmod 755 {} \;
find /home/user/public_html/ -type f -exec chmod 644 {} \;
The first line corrects ownership. The second perms on directories and the third on files.