So the only secondary menu that can be set with theme, you can check on http://themes.muffingroup.com/be/charity/ (right top corner). This menu can be set instead of social icons under Appearance > Menus > Manage locations section.
Like we wrote above, you need to create simple menu first under Appearance > Menus section and then under Appearance > Menu > Manage locations, you need to set this menu under right option.
I have already created a new menu named "Secondary Menu" and I have selected this menu in the Manage Locations tab so that "Secondary Menu | depth 2 (Header Split 5)" points to my Secondary Menu.
As you can see on our demo, additional menu which is in the right top corner, displays on Action Bar section. You need to activate this bar under Theme options > Menu & Action Bar > Action Bar section then.
Comments
what do you mean by saying "secondary navigation"?