Since release 2015.10, eZ Platform is very close from the standard Symfony distribution. It comes with default settings that will let you get started in a few minutes.
Most projects can use the provided AppBundle, in the src folder. It is enabled by default. The project's PHP code (controllers, event listeners, ...) can be placed there.
Reusable libraries should be packaged so that they can easily be managed using composer.
Project templates should go into ezpublish/Resources/views.
They can then be referenced in code without any prefix: ezpublish/Resources/views/content/full.html.twig can be referenced in twig templates or PHP as content/full.html.twig.
Project assets should go into the web folder, and can be referenced as relative to the root: web/js/script.js can be referenced as js/script.js from templates.
Configuration may go in ezpublish/config. However, services definitions from AppBundle should go into src/AppBundle/Resources/config.
The recommended method is to version the whole ezplatform repository. Per installation configuration should use parameters.yml.