How to manage Menus in One Page and Multi Page templates as same menus?
For having 2 menus in One Page template and Multi Pages templates as same menus follow this instraction:
You should create 2 menus, one menu for your one page template (as a One Page) and another menu (Main Menu) for all other pages. (Assign each menu to each Theme Locations in Menu Page)
in One Page menu you should link the items to sections by anchor link like this: #YourAnchor (Custom Links)
in Main Menu you should use full URL like this: http://www.YourWebsite.com/#YourAnchor
For more information about One Page template you can read the Documentation file. (Documentation file included in your downloaded full package, not installable WordPress version)