The details shared here apply to the most recent version of Flex. To keep your theme up to date, check out this helpful document.
Color Settings per Section
In addition to the site wide color settings (Customize > Theme Settings > Colors) the Flex theme also includes additional color settings per section for more granular control over your shop's look and feel!
If you head into a section, you'll see additional color settings with color pickers. These will be transparent by default, but if you'd like to override the site wide color settings and select colors for that that specific section, you can simply select new colors in the color pickers.
If at any time you'd like to revert these, you can just click 'None' in the color picker, and the colors will fall back to the default site wide color settings.