The additional single pages should auto-build the menu for you based on the page sections chosen and any page links you have chosen to display in the metaboxes of the page edit window (below publish button of the page). The WP menu set will be ignored since the page navigation links for the additional single pages can be different.
Having said this, I understand this situation is not always ideal for everyone and hence have come up with an update to set a custom built WordPress menu for each of the single page websites. Will submit the update today and you should have it in a day or so. Thanks