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I did find this breakdown of the folder structure
So, if I want to add a domain to my server, in Ensim, I just click Add Site, and specify the admin name and password, and site name. To do that without Ensim, I SSH in and I go to home/virtual/ and add a directory with the name of the site?
Don't take this the wrong way, but a dedicated server may be a lot to take on. If you've had no formal training it might be easier to start with shared hosting, then VPS to familiarize yourself with all the pieces of server administration first.
It seems like there would be book or something that outlines all this stuff. I've read a few but they are usually too advanced. I'd like to see a more beginner's version.
There is a huge learning curve when you first get started. If you are new to Linux, then I would not start with trying to setup hosting. If you are not careful, you could open up the system to security risks.
I recommend starting with some Linux basics, like how the file system is organized, how services are managed, where configuration files live.
The Dummy series of books are actually pretty good for starting.
Also, I would just get a copy of VMware Workstation for your desktop. Download a copy of CentOS or other linux distribution. I recommend CentOS as it is like Red Hat and a distro that you would likely use in a production environment.
You can then have a local test environment with easy rollbacks etc.
If you are really serious, consider taking a class somewhere. Many community colleges have IT courses in Linux and there is always online training from places like Red Hat.