Since SiteAssist creates the menu contents and links based on the site you are creating you will not be able to craft the menu separately from the structure within the interface. Because of this you may need to craft your menu separately with Menu Writer and manually add it into the template that SiteAssist creates or you can edit the existing menu that is created with the SiteAssist site using the buttons from the property inspector. You would want to craft the contents of your menu to match your site and the layout you would like.