Consider the Color Manager as your color palette, where all the colors you need is set in there before you start painting.
The same thing for Font Manager (but for fonts), you need to set the fonts that you're going to need before you start your design (or add a font along the road if you need to).
Now navigate to Theme Options > Typography turn on the FONT MANAGER option.
Set the BODY FONT and BODY FONT COLOR, you'll see your list of font and your color palette in there. Do the same thing for HEADINGS FONT and HEADINGS FONT COLOR, that will be now your body text and headline's font-family and color defaults.
If you did not set a specific color or font-family on your Element, it will automatically
inherit that default (unless you have a custom CSS that interfere with this inheretance).
Hope this shed some lights,