Hello,
Both cPanel and Plesk require separate/clean servers to operate. Each control panel provider have support areas where you can manage and secure the software and related services. WHT also has a tutorials section which will likely include a tutorial for securing/optimizing your Virtual Server, but a lot of management boils down to experience and research.
Both control panels have backup options in the software.
Here's an old thread for VPS optimization -- it may be a little dated but you can read through it.
http://www.webhostingtalk.com/showthread.php?t=468168
Good luck!