The following are a few security tweaks you can do to your dedicated server if you are running cpanel / whm. The following changes are made in the web host manager.
1. Login to WHM as root.
2. Server Setup Tweak Security
3. Enable php open_basedir Tweak
4. Enable SMTP tweak.
5. Optionaly enable mod_userdir (This will let your users preview their site at your_main_domain/~username)