If your employer is so against using tried & true open-source technologies then perhaps you should reconsider..
But, if you choose to move forward, the best resources I can offer would be:
Organize your application like a Ruby on Rails application - it's just a very nice way to organize things:
- application
- public
- vendor
That's the basic application structure I've used in the past when developing custom MVC frameworks. At the root level you would have a .htaccess file that would define your rewrite rules to forward all requests to the appropriate controller/action.
In so far as the views are concerned, I've had very good experiences with Smarty in the past. It's a very solid framework and it has plugin support, caching, and a fairly robust settings system. And, it will fit nicely into this structure. The only annoying (at times) thing with Smarty is that you can't have inline PHP code in the templates.. if that's a deal breaker, then perhaps just name your view files *.phtml so you know for certain it's a view and have it use straight PHP.