With my capt apps, I do most of the development and testing using the desktop safari browser, and then move onto testing on actual devices later on, once I’ve got the app mostly working. I use this fragment of code to detect if I’m running inside phonegap, or if it’s a desktop browser, and then instantiate my app appropriately.

function onDeviceReady(){
  window.app = new Application;
  app.start();
}

if(window.PhoneGap){
    document.addEventListener("deviceready",onDeviceReady,false);
}else{
  $(document).ready(function(){
    onDeviceReady();
  });
}

The window.app style of encapsulating my apps has worked well for me in apps I’ve built using capt and backbone, I still haven’t got to the point of encapsulating everything (all classes are copied into the window scope for example).