Several posts mention online manuals for various control panels, such as Cpanel and Webhost Manager. I am looking for an manual that explains how do basic things without using a control panel. For example:
--How do I set up online statistics?
--How do I add in a second domain?
--Is it safe to move my timeouts from 5 minutes to 1 hour?

Are there online manuals that explain these types of issues?

Well, now it is going to depend on what OS you have installed now isn't it? If you want general apache info there's http://apache.org also you can search for 'newbie linux' in just about any search engine and find some basic info sites. As for specific questions, you can try posting here, and maybe someone can direct you to the proper URL(s). It helps to know exactly what you are running.