Go to backend menu Habi > Habitheme > Theme Settings.
Click the Configure button on the design you are using.
In the section General > Header, go to field General > Main menu and select the menu you want to use.
Please remember to refresh the Magento cache after changing the menu (System > Tools > Cache Management).
Besides, in the General group, too, there are other fields relating to the menu section of your website.
Go to backend menu Habi > Mega menu > Mega menu.
Choose the menu that you want to edit.
In the edit page, go to section Menu builder, you will see a builder with 2 columns. To build your menu, you only need to drag the elements form the left column to the right column.