A bit confused on what these web scripts are. Are they the install scripts for things like Wordpress, YaBB, Agoracart, etc under "Install cPAddons Site Software"? I have a few installed (YaBB, Agoracart and PHPMyChat) but don't think I ever use them. Would I update them under "Manage cPAddons Site Software"? Would I even need to if I don't use any that are installed or would that possibly compromise the security?
Found the PHP and MySQL update directions in the Knownhost tutorials and I am assuming those are still pertinent even though they are a bit dated. Would they still be pertinent if I had my PHP changed to suPHP? Number 7 - (7. Select required PHP version and PHP options that your applications may need I hope I can simply leave the default choices here as I have never changed it....
Lastly, and probably most importantly, how would I know when to install the PHP, MySQL and Apache updates without compatibility issues? Are they similar to almost any computer update where you give the release a few iterations to work out any bugs?
I use the term web script to define any pre-made code you use on your website. cPanel provides installers for those scripts but does not automatically update them. It is a good security practice to either password protect, or remove anything that you don't use when it comes to pre-made code. If you don't keep up with updated releases then it will eventually fall out of date and have the potential for an exploit to exist in the code.
However, if you want you can simply open a support ticket with us and let us know what you would like upgraded.
Generally speaking MySQL and Apache don't have to be updated very often.
Apache its self has very few if any compatibility issues when going from version to version, so it is safe to keep this at the latest version of your branch. (2.2.X or 2.4.X)
MySQL is very much the same way. In regards to common scripts MySQL has not made many changes that would cause problems, there are a few things that changed between 5.1 and 5.5 (5.5 being the latest) but primarily you won't have to worry about upgrading MySQL near as often.
PHP is what generally gets developed on and upgraded the most. The problem with PHP is they constantly add and remove what they consider to be "valid" working code. So a php script written for php 5.1.X may not work in php 5.4.X. If your upgrading from say 5.4.6 to 5.4.21 then you'd be safe, as code is not changed in minor releases. Generally these are security patches and bug fixes. It is only when you go from major releases (i.e. 5.1 to 5.4) where you may see compatibility issues. Good news is, if an upgrade causes issues you can generally downgrade until you isolate them.
I would agree to an extent about your analogy with computer updates. Wait a little bit, ensure they are stable and then apply them. The only other step would be to look @ any software your using to ensure that it is also compatible with it, primarily in regards to PHP.