There are 2 common methods:

1) Your theme has its own CSS file and you can edit that file (typically named styles.css)
– OR (if applicable) –
2) your theme may have a Theme Settings area that allows you to edit the background color of the header or footer (sometimes through the Visualizer)

Regardless, HFCM plugin has nothing within it that would change your header / footer background color.

Hope that helps.