PHP PDO prepared statements

Question

I was told today that I should really be using PDO and prepared statements in my application. Whilst I understand the benefits, I am struggling to understand how I implement them into my workflow. Aside from the fact that it makes code much cleaner, should I have a specific database class which houses all my prepared statements or should I create one each time I want to run a query? I'm finding it very hard to understand when I should use a standard PDO query and when I should use a prepared statement. Any examples, tips or tutorial links would be greatly appreciated.