The best way to do it is to create modules for all the parts you want to integrate in your custom extension. There you can do whatever you want with PHP and set template variables to use with your custom templates.
Actually the eZ Publish kernel is built on modules. The best way to learn is to read the source (kernel/*).
Some references:
- http://ezpedia.org/wiki/en/ez/developers#eztoc346_6
- http://ezpedia.org/wiki/en/ez/module
- http://ez.no/ezpublish/documentation/development/extensions/module/module_tutorial_part_1 - http://ez.no/ezpublish/documentation/development/extensions/building_an_ez_publish_module
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