Thanks for writing in.
This depends on where is the source of your fonts is. If the fonts that you have are on Typekit, you can use X's Font Manager to add your Typekit fonts to your site though even if you are not using Typekit, it would be best to use the Font Manager so you will be able to manage your site fonts easily and in case you will need to change the font, changes in the Font Manager will take effect sitewide so it would be less hassle to do.
Since you mentioned that you already read the KB articles about the Font Manager, what you have to take note is that one you added the font in the Font Manager, when you go to the Theme Options' Typography setting, the fonts you have chosen will be available in the font setting options like the Body Font.
The fonts you chose will also be available in the element font settings which are the elements you use in Cornerstone.
For example, if you chose a font and named it Body Font and you chose it in the Theme Options and some elements but later on you decide to change the font, you could simply go to the font manager and change the font assigned to Body Font and it will update all of those settings you previously set automatically.
Currently, the Font Manager could handle system fonts (fonts that are installed in your computer by default), Google Fonts, and Typekit fonts (if you add you typekit ID in the font manager setting). If the fonts you are trying to use are offered by those services, you can simply pick then in the font manager.
In case the font is not there (related to your second question). you can manually by using custom CSS.
Here are some threads related to this:
Hope this sheds light to your questions.