My experience: I've built 5 sites with eZ publish 2.2.x and to do what you want to do, I *had* to dive into the PHP code of eZ publish. I can assure you that you don't want to do that!
It's not that the code is bad (it's written very cleanly unlike most other open source CMS), BUT you will run into big problems, if you want to update the system to a new version of eZ publish which you will want to do in the future. You will have to track down all the changes you did and do/adapt them again.
Even though this problem can be circumvented, you will have much better (and more portable!) results by using the templates (which should stay compatible with new releases).
The new template system is great and gives you a lot of power. Use it!
Just my 2 cents.
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