Looks like whatever is setting the custom bar is giving it a low CSS Z-Index. That means anything with a higher Z-Index ( such as the navigation bar ) will appear above or on top of your fixed bar. You should be able to add the below custom CSS to
Appearance -> Customize -> Additional CSS
.ht-site-header .ht-top-header { z-index: 100 !important; }
This should overwrite the inline z-index and your fixed bar would appear above or on top of your main navigation when the user scrolls to that point.