I have implemented a mechanism of setting a custom menu defined in WP admin for additional one page templates since the current implementation just creates a auto-built menu for additional pages which use “single page site” templates. This change just needs a slight polish in terms of how to treat the home page and single pages which are not home pages. I will post a private message with the files in next few hours which will let you choose a custom menu for a page. That change will be part of next update to the theme. Thanks.