You can do this pretty easy. Make sure you have the Cover selected on the left. Then click the Color square on the top menu bar., which says "Paper Color".
Once you click "Paper Color", pick a color and press "Ok".
You will see on the page view side your cover color updates. In the workarea you do not see the color there. If you downloaded right now, the paper color would be (in this example) red, even though you don't see it in the work area.
In order to see it, you need to click on "Cover Template Opacity" and check the box, "Hide Cover Template" and then you will see the paper color in the work area.
It should look like below once you did that.