1- Login to Contao
2- Go to Themes Edit > Edit the Frontend Mdules (Two icons before the last icon)
3- Click on the edit icon (pencil) of the Menu to Edit > Edit the start and stop navigation Levels
4- Select the Reference Pages
5- Make sure if you add new pages that these have a class assign because contao assigns Styles to the links on footer and manin menus and the links may not appear if no style is assigned.