As a newbie of Zend framework, I have a few version-dependent questions on the framework.
No, you have pretty much control over everything, from locations to notations.
The recommended structure has pretty much remained the same for a long time. Sometimes there can be some new features that can improve the structure a bit (such as resource autoloaders), but essentially it's the same. And even with such improvements the old structures remain backwards compatible.
See previous answer.