Napa was created with the objective to facilitate a 'lightweight, in-browser experience' to build SharePoint or Office web app in the same browser where they would run. Ergo, it was designed to kind of complement the inherent features of the browser.
For advanced tooling, one would have to turn to Visual Studio 2012.
You can debug code like any javascript: In IE, 'F12 developer tools' could be used to debug the JavaScript, HTML, and CSS.
Unfortunately, at now, the 'Napa' is only for development and deployment packages, no resource debug.
I hope you understand. Maybe who knows what the future may arise this feature.
Reference:
Fórum Ninja
MSDN
Edit:
You can download Project Napa(the format is filename.exe):
follow step-by-step:
Download: 
Execute file downloaded: 
Wait for some seconds, will open vs 2012: with VS 2012 opened, set connection to online. 
Usually they come pre-configured, after do made last step, break point in your code and start mode 'debug'. :)
sorry my bad english.
hope this help.
$.ajaxor$.getJSONit won't work... you need to use a cross domain technique of somesort likeSP.RequestExecutorsince your app is actually in a different domain than your host. You'll also need to grant the appropriate permissions in the app manifest.SP.AppContextSitewith your host web address with the help of the RequestExecutor library -- so that SharePoint sets up a special proxy for you. Here is an example: msdn.microsoft.com/en-us/library/office/… -- search for cross domain on this site or post another question if you still need more info!