How can I make my Linux box (cPanel/WHM installed) more secure?
It's a large question so I can only show you a points where to start look to.
1. Look at your firewall settings. Make sure that your default policy is drop or reject, and you allow only needed ports from outside.
2. Make sure that your SSH configured to use key-based authentication or 2-factor auth instead of it. Configure fail2ban is also a good idea.
3. Make sure that your system and software is up to date and all security patches are installed.
4. Make sure that your software (apache for example) is running NOT with root privileges.
5. Make sure that your config files have correct file privileges and regular users can't access them.
6. Check your logs for any intrusion signs regularly or configure email notifications about that.