dansup, you do it in your theme, it's normally in an xml file somewhere in res/values. Like this:

<style name="..." parent="...">
    <!-- ... other attributes you most probably have there ... -->
    <item name="android:enforceNavigationBarContrast">false</item>
    <item name="android:navigationBarColor">#FFFF00</item>
</style>

Can also be done dynamically in an activity, getWindow().setNavigationBarColor(0xFFFFFF00);