How to structure Javascript architecture to compliment a PHP MVC web app?

Question

I am working on a new JavaScript architecture for a web app iteration. The previous iteration had lots of inline code, scattered includes, no directory structure for .js files and everything was in the global namespace. I am aiming to: keep the script includes in the footer, keep everything in an application namespace/object, add organization to the .js files and minify all the application specific files in to one bundle.js

I am trying to take a modular approach based on Nicholas Zakas: “Scalable JavaScript Application Architecture” http://www.yuiblog.com/blog/2009/09/17/video-bayjax-sept-09/

the site is currently structred like so

/app
 /models
 /views
   /home
   /auth
   /meta
     about.tpl
     contact.tpl
     privacy.tpl
 /controllers
   home.php
   auth.php
   meta.php
 /public
  /js
   core.js
   /modules
     module files here
   /jquery
     jqueryplugins here
   /controllers
     home.js
     auth.js
     meta.js

the controllers have methods which correspond to our url routing and view rendering. For example http://localhost/meta/contact would call the "contact" action on the "meta" controller and render the meta/contact template.

I am planning the js architecture around a single initialization call to the apps global object passing it the controller and method as arguments i.e.

localwebapp.init(controller, method);

At this point in the design I am struggling on inheritance and module implementation. Some modules will be global and be used throughout all the site, some modules will be used through out specific controllers, and some modules will be on controller actions only. Modules are independent and will not communicate with each other they will need to be assigned to a "sandbox" which they will check with for event triggers

I'm thinking I will need sandbox and module classes. The controller scripts will basically be a few lines of modules being assigned to the sandbox and initialized.

Let me know if I am reinventing a wheel here. Any direction is much appreciated. I have looked in to javascript MVC frame works like JavaScriptMVC but it looks like it is not what I need