Once of the nice things about running a LAMP stack is that you don't have to worry about tracking the versions of any packages. So long as you keep up with repository updates, you automatically get the latest operating system and software updates for every piece of software on your system. The maintainers of each package worry about security and version updates. Also, dedicated is the way to go for your web server. You will absolutely get the best performance that way.
If you're new to the command-line, Unix for the Beginning Mage should help you get a good grasp on the basics. One of the best features of modern Linux distros is their package management systems, which you should also be very familiar with. In my (obviously biased) opinion, Debian's Advanced Package Tool is by far the best. You can find a good APT tutorial on the Debian Wiki.
Edit: The Unix for the Beginning Mage link seems to be broken at the moment, so I attached a copy of the PDF to this post.
I got used to the Unix terminal because of first getting a taste of Debian's Apt, thanks to SSH'ing Media Temple's Dedicated Servers a while back (of course it's still all different commands, but I wasn't a shell person at first of course). I worked with homebrew to get some packages installed on this Mac, and I do with with curl and whatever's necessary to make & install.
Here's a reason why I preferred using the GUI for packages such as MySQL. I removed "root", or changed, and all passwords on every database 25 characters generated. That's why I prefer seeing things first hand because I don't do simple security either.