Header builder allows you just to choose location on your menu by drag&drop the Menu/Secondary menu elements and choose what menu to show from the list of menus that you created in the menu element settings. Did you watch the video on how to create header using header builder?
If you need to edit menu list itself you need to do this from Appearance > Menus.
Does plugin that you use require any special settings like menu location?
Provide us with WP Dashboard access to your site for better understanding settings of your plugin.