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I have recently started working on an eCommerce site for a company and they have selected Magento 1.4.0 to run their store. I have spent most of my PHP "career" working with various MVC frameworks (even Zend with Magento is supposed to be based on) but the complexity of Magento seems to be on another level with no seemingly good resources to look to for help.

Looking around the site I have seen suggestions for certain books to use as reference, but they all refer to Magento 1.2 or 1.3.

My goal is to develop for Magento in a way that I do not alter any of the base code so that the client can easily upgrade the version of Magento and just "drop in" my code and have it work. The current issue is how to properly use the layout/template breakdown correctly and how to add custom model/controller functionality to the application without hacking away at Magento's core code base.

A: 

how to properly use the layout/template breakdown correctly

What you need to know is the folder structure of the Magento & the use of its own MVC structure. This is a very very important part to get you started from the basic roots. Whatever version you use, the folder structure & the MVC structure followed by Magento will almost never change. Try to follow the Magento's own Knowledge Base & Wiki tutorials. If you want you can also follow some other sites as well.

how to add custom model/controller functionality to the application without hacking away at Magento's core code base

You will need to use the custom module functionality to override the core code base of model / controller. It's a simple process of writing the main logic in a XML file, of what core class you want to override of Magento, in your module's "etc" folder. Try to understand the process first, from the Knowledge Base & Wiki tutorials, to get a firm grip on overriding core classes.

I hope this helps.

Knowledge Craving