2 css files? Theme css file gets override by another css file that I can not edit

Make the CSS rule of style.css win over the rule of the other file.
To do so you can add the selector of a parent element of #header, or an !important after the color.
These two examples would work:

body #header{background-color:#ffe600}

#header{background-color:#ffe600 !important}

Better adding the selector of a parent element, rather than adding an !important.