There is no dependency between the structure of the Alfresco source code and the structure of your project that contains your Alfresco Explorer customizations. In fact, unless you are helping Alfresco develop the Explorer client, your Explorer customizations should be done entirely separately using the extension mechanism. As a general rule, you shouldn't have to recompile any of Alfresco's source to build your customizations.
You should set up your project structure how you see fit with the Alfresco SDK JARs as dependencies so your code will compile. Then, decide on a deployment strategy. You can either produce an AMP and then use the Module Management Tools (MMT) JAR to deploy your AMP to the Alfresco WAR, or you can simply copy your extensions into the right places within the Alfresco WAR. I use both–it depends on the type of customization I'm working on.
The Alfresco wiki [1] and the Alfresco Developer Guide [2] are both good places to learn how to set up the SDK in your development environment.