You should not have any jQuery mobile code in your controllers or models.
I'm not sure what exactly you mean by "I want to know if there is a way to separate view controllers and models in jQuery mobile" - this is all PHP, jQuery mobile should exist only in your views.
Just create a normal MV MVC setup and use jQuery for mobile in views.
I used jQuery mobile on rails site and just created .mobile and .tablet view for each page. jQuery mobile only affects the appearance, its pure look.
edit: There were a few more rails that ran "mobile or not", but since you are in php, which is not worth delving into.
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