Your mobile app is not part of your website, so you need to create a RESTful API on your web server that your app can use to exchange information with your server. There are many approaches, all of which are outside the scope of this forum. I recommend you search places like HTML5rocks and similar sites that can educate you on how to build a web API and how to interact with that API. You can also inspect the XDK web services component to see examples of how it is typically done (note, the web services component is a convenience that takes advantage of existing web service APIs, the XDK does not control those web service APIs).
Check out the documentation for this Github project called sandman2. It utilizes RESTful API to access and send to servers. There is a list of compatible server types and database types. If you already have a database for the website, it should be fairly easy to integrate sandman2 to your database to then use for your app - to both push and pull from this database. >https://github.com/jeffknupp/sandman2<