Sorry, but I don't clearly understand your questions, however you should read something about OOP (object oriented programming :P), ORM and programming patterns, like Active Record or Table Data Gateway, Row Data Gateway, DAO (Data Access Object), etc.
Also read some on offical ZF's manual about Zend_Db (as I remember it's build upon a clear example of bug tracking application)
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Where am I supposed to write the logic that stands between Model and Controller ?
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Model represents data from the databse. In controller you should initialize model and access its methods to get data (which model previously queried and formed into desired form - eg. Menu::getMenu() will return array containing menu items).