Actually, the way Pro header/footer builder works is that you will need to have a separate element for mobile view and desktop view because the navigation in desktop view is in line and the navigation for the mobile view is the collapse element.
There is an option called hide during breakpoint which you can use to hide or show a certain element in desktop or mobile view. The template that you used utilized that feature, so you will need to go to the mobile-specific element and set the proper menu there.
I suggest that you read this and this articles for more information.
If you want to have more information regarding the specific elements used in the template I suggest that you check the articles in the elements section of our knowledge base.