Improved one pager
If you need to find a way to make the primary navigation links scroll to the section the same way the side navigation does when it appears as you scroll through the site, you need to do these custom tricks.
First of all, your navigation menu items should be custom links with hashtags, for example:
<a href="http://yoursite.com/page#part1">http://yoursite.com/page#part1</a> <a href="http://yoursite.com/page#part1">http://yoursite.com/page#part1</a>
You should create your menu using links like above.
Second, you need to go in that page you want to use and add these "parts" in the DOM. To do this, use the classic HTML editor of the page or insert RAW HTML shortcodes.. Anyway, you need to add empty elements wherever you want those parts to be. For example:
If you post the above code somewhere in your page (again, it needs to be HTML, not using the Visual Editor), when you'll click the #part1 link, it will take you to that area. Of course it won't scroll nicely, but it will take you to the proper place.
Use this technique in almost any theme and it should work.