Not that I'm an expert on Centos, I use mandriva....
1) It's different than windows. The gui is just a program, running on top of linux. You can change the gui, or not run one at all. So the existence of a gui doesn't mean you don't have a server edition. It probably just means you have server software with a gui. I use the identical software on my server and desktop except on my server I don't bother installing the gui. But even saying server edition is a bit misleading. All linux is a server edition. People just tweak it differently for different uses, install different things. I install a gui and games on my desktop, I install apache on my server.
2) It should mostly apply I think. Further, general linux material should apply. The primary difference between linux distributions isn't the programs, it's simply the directories where things are kept. If I switched to centos everything I have now is likely there,just in different directories. But generally, apache is apache, shell commands are shell commands.
3) decide if you are going to administer the server using a cpanel, or directly at the command line. Then I would start administering the box from your windows install, as if the server were remote. i.e bring up the virtualbox install, then go back to windows and operate it from there. Probably a good first exercise is to take your existing website and get a copy up and running on your pc. that'll get you familiar with installing software, setting up apache/php/mysql and some common command line programs.