Modules allow you to separate your application into specific concerns. Frequently my larger applications will have a default module for users and an admin module to contain all administrative functions. I use the directory structure recommended in the Recommended Project Structure for Zend Framework MVC Applications -> Module Structure section of the Zend Framework Documentation.
As to your second question, the answer is yes and no. If you want to take advantage of the default autoloading functionality (loading Admin_Form_Settings from the admin/forms directory), you will need a bootstrap in each module. See Matthew Weier O'Phinney's article on Module Bootstraps in Zend Framework: Do's and Don'ts for more info. You may also want to Google for and review Rob Allen's post "Bootstrapping modules in ZF 1.8 and up."
Answering no to your second question: one technique that I like to use that doesn't require empty bootstraps in each module is placing all of your application classes in the application's lib folder, and mimic the Zend Framework's directory structure. If my application is named Example, I'll create a folder named Example in my /lib directory. My user registration form would be placed in /lib/Example/Form, and might be named UserRegistration.php. My class would be named Example_Form_UserRegistration. Autoloading my form would require the following in the Bootstrap.php file:
protected function _initAppAutoload() {
$autoloader = Zend_Loader_Autoloader::getInstance();
return $autoloader;
}
My application.ini would include the lines
resources.frontController.moduleDirectory = APPLICATION_PATH "/modules"
resources.modules[] =
autoloaderNamespaces[] = "Example_"
Using this technique you should then be able to autoload any class in /lib/Example anywhere in your application without placing empty bootstraps in each module.
NOTE: I tried posting links directly to the docs and to Rob Allen's article, but since I'm a new guy I was only allowed a single link. Apologies for asking you to Google items that should be links.