how to retrieve query_vars by sending custom url to Wordpress by Ajax

i am working on a new wordpress theme that will convert a wordpress site to a SPA (single page application) .

This theme works by JSON REST API and Backbone.Marionette.

I use backbone.Marionette and jquery for client-side action. but i have a problem by wordpress links (pages ,posts , custom links in post contents)

how can i setup a structure on my theme to convert all links to query_vars without sending links by http to server .

must i use

$wp_rewrite->rewrite_rules;

and use the rules for my Appliction.AppRouter.

thanks a lot