it is recommended to structure entire code base (config, osgi services & components, wcmuse classes) inside lazybones structure i.e. ui.apps and core. As we have a predefined template that we are using for creating the project in aem. It has option to create only two packages ui.apps and core. Once project is created you can create addition packages as per your need.
If you want that lazybone template give you additional optional to create extra package . Then in that case you have to write custom lazybone template.
For more information on lazybone you can visit http://www.aemcq5tutorials.com/tutorials/create-aem-project-structure-using-lazybones/
