HTML, CSS, and JavaScript/jQuery are mostly front-end tools, and it sounds like you want to get more into back-end stuff. It's still good to know them, of course, but it's good to focus on what you really want to do.
You'll need to know at least 1 server-side scripting language (2 or 3 are better, but you don't need to know it all). These include things like PHP, Ruby (and Ruby on Rails), .NET (I think), Java, etc. There's also Node.js, which is JavaScript as a server script (it's normally a client script), but I'd suggest holding off on that one for now.
You do NEED know know about FTP, hosts, domain names, servers, databases, etc. These are your tools. You should also find a good text editor, like Sublime Text or NotePad++.
cPanel is good to learn, since many hosts use it. Most also use MySQL (or another form of SQL database). It's also good to have an understanding of how mobile apps work.
One of the books I remember is Concepts of Database Management by Pratt and Adamski (6th edition seems fine, presently). It mostly uses examples in Microsoft Access (which has some minor variations from web-oriented SQL), but it does teach SQL.
Websites you might find helpful include Codecademy.com (free), TeamTreehouse.com, and Lynda.com. If you get stuck on things, Stackoverflow.com can often provide answers or work-arounds.