On the “Non-Profit” advanced demo Where do you change the color that is behind the menu items. (Green for this sample)… 
Hey There,
In the Theme Options under the CSS section you will find following CSS code:
.x-navbar {
border-color: transparent;
background-color: #00a580;
}
By changing the background-color value you can change the color of the navigation. All the best!
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