It is best to use CSS that can be easily adapted for multiple site configurations using a range of different theme preference colours. The colour preferences page contains colours such as: primary_colour, secondary_colour, accent_colour etc and can be found in the backend at: ../configure/website/appearance/colours
These can be used in the css files in your theme as shown here:
header {
background-color: {{ theme_preferences.header_background_colour }};
}You can see a full list of the available colour options here.