This is how I would structure it:
Use HistoryJS to manage the URL. JS pushstate browsers got full correct URLs and JS non-pushstate browsers got hashed urls. Non-JS users went to the full URL as normal with a page reload.
When a user clicks a link:
If they have JS: All clicks to other pages are handled by a function that prevents the default action, grabs the HREF and passes the URL to an ajax request and updates the URL at the same time. The http response for that ajax request is then parsed and then loaded into the content area.
Non JS: Page refreshed as normal and loads the whole document.
When a page loads:
With JS: Attach an event handler to all your links to prevent the default so their href is dealt with via Ajax.
Without JS: Nothing. Allow anchors to work as normal.
I think you should definitely have all of your content accessible via a full, correct URL and being loading it in via ajax then updating the URL to reflect the address where you got your content from. That way, when JS isn't running, you don't have to change anything.
Is that what you mean?