How are you adding your classes to the diagram, are they simply a drag and drop from the project explorer, or are you reverse engineering the code into the model? If you are just dragging and dropping then the auto layout button mentioned above is what you are after.
If you are importing the classes automatically from reverse engineering then you have two options.
In Enterprise Architect under Tools -> Options -> Source Code Engineering there is an "Auto Layout Diagram on Import" drop down. By default it is set to auto layout your diagrams only when a new diagram is created. If you are creating a diagram before importing the class you can change the drop down to: "Always". Keeping in mind that although you are working in Eclipse, Enterprise Architect's engine is still responsible for the modeling work in the background.
I hope this helps.