So your page structure for your mobile app is just one HTML file with all 'pages' as div's or sections within that HTML file?
You should only reference your js and css in the HTML file(s) that you'll be accessing with your mobile device, which if I understand correctly will just require you to reference them once.
It makes it a bit easier to think of the js (jQuery) and css as merely extending the function and style of a webpage / application, like branches on a tree where the main HTML file in this case is the tree trunk.
I'd like to draw you a picture of a tree but it would probably detract from the point I'm trying to get accross.
I hope I haven't confused you more...
