Help With Apache on Server

Okay, I'm good with dedicated servers, but Apache isn't my thing =S. I've researched this but haven't found a good guide, so I figured I'd turn to the community here at V7N.

I have a server, with cPanel, dual Xeon, and so on.

Here's the problem:

How do I add a website to Apache itself? I don't want to add a website via cPanel for reasons. Can someone give me a complete guide to it? I want to have SSL support, everything.

Also, how do I setup nameservers for my server outside of cPanel? Do I just create nameservers at my domain registar pointing to two IP's on my server that are available, and point my domain name to it, or do I have to do some work on Apache/BIND's side too?

ALSO, I still want to use the domain created outside of cPanel with cPanel as the server hostname. Let's say domain1.com will be the site I want to create outside of cPanel, but I also want the hostname of cPanel on the server to be server1.domain1.com.

As I said above, I want the nameservers that domain1.com will point to to be created outside of cPanel.

How do I do this???:shock::shock:

**If you want an idea of what I'm talking about, visit a site hosted with HostGator, and you can access cPanel, etc. via port 2082 or /cpanel whatever. But if you visit hostgator.com, there's no port 2082 or /cpanel, because the site isn't on cPanel. I want a setup like that basically.**

P.S. I'm using Apache 2.2!