At the point you're talking about, you want more of a "How to administer a Linux Server", since that's what you're doing.
CPanel, Webmin, and all of those types of tools are abstraction layers that you're dispensing with. When you go below those, it's core administration, which means learning to fiddle with the knobs of the various softwares running the show. This includes things like your MTA (sendmail or postfix, probably), your web server (probably Apache, though maybe nginx), the interpreted scripting language (php or maybe perl), plus all of the other fun bits that come with server administration that you mentioned, like user administration, network configuration, storage management, manual backups, etc etc.
Does it sound like fun? If so, you're a sick person (and welcome to the club).
I would recommend a general purpose Linux admin book. If you've got a CentOS OS installed, you could do a lot worse than Red Hat Linux Unleashed (Redhat and CentOS are essentially identical, for the tasks you'll be accomplishing). There are equivalent books for whatever OS you end up with, so do a search on Amazon. If you update with the distro you're running, I'm willing to bet that some people could offer good suggestions.
It's a big can of worms that you're talking about opening. Make sure you're really interested before you dig in. The rabbit hole is deep.