I don't completely understand Servers and I can't seem to understand them [on hold]

I am a pretty good front-end web developer, and I have recently started developing back-end stuff. I bought a domain name and server space with godaddy and I am confused about a few things. When I first entered access to the server, I was greeted with cpanel. I know what that is, it's like an overlay, training wheels if you will, for a web server. I don't completely understand the server itself. Through cpanel, I can add databases, transfer files, and do a bunch of other stuff I could do through the cmd line, but cpanel turns it into a GUI. So one of my questions is, let's say I remove cpanel. What do I see now? Like for example, how would I do databases? Would mysql still be there? And if so or not, how would I know if there is nothing to look at? I'm pretty sure servers run a linux distro, but i'm not sure how that works. Is there any way to see what is happening? And if so. I don't really understand what I don't understand, so pardon me if it is confusing. Can anyone point me to a website or article I can read to better understand running this web server and learn how it works? Thanks.