@thgr, A theme (and installed plugins) may have several elements for which the background-color is set and needs to be altered with your own preferred colour. A few of these elements are #head for the header, .card for the list of items in a blog, etc.
In ‘/user/themes/mytheme/css/custom.css’ try the following:
You will have to explore your site and for each element you wish to change the background of, you need to find out the selector (id, class, element) and add that to the list.
You can find the selector of an element by right clicking the element and open the developer tools of the browser (‘Inspect’ in Chrome).