I assume that you are using CI as the backend for delivering data back and forth between your mobile application created using phonegap + jquery mobile. If so, regardless of whether you use CI or some other basic web frameworks, it should be pretty simple. You probably want to use JSON as the data format to keep the data size.
I would suggest that RESTful web services work well for you. Check out this guide to work with CI: http://net.tutsplus.com/tutorials/php/working-with-restful-services-in-codeigniter-2/
I personally use CI + phonegap + xuijs stack now and its pretty straight forward in terms of communication.
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