On the Leaseweb Labs blog there's a recent post looking and some of the things you can do to optimize Zend Framework and Doctrine when used together for database access.
In principle, the combination of Zend Framework with Doctrine is not too difficult. But first let's talk about the preparations. According to the author of Zend Framework, the default file structure of project can be a bit more optimal.
They start by describing this optimized file structure (moving the models out of the modules and into the library) and what you'll need to change in Doctrine's configuration to make this work. The post also includes examples of what the larger config should look like when the changes are made. They show how to extend the default Doctrine CLI tool to make a custom "sandbox" instance and show some tuning you can do on the Zend Framework side so it can optimally work with the new models.