The color chosen will be the background color of your tabs and accordion headers.
This setting in combination with the 'body background color' gives 2 color background schemes to your templates.
Note that in the case of tabs, the 'body background color' also affects the headers: the non-active tabs will get the 'body background color'.
Have a look at the color schemes demo for examples of how these colour combinations come together.
Header background color setting is a basic configuration option.
Here is the list of all basic configuration options.