When setting up new projects, the structure or hierarchy you need might not fit the standard project templates available in CORE. How to handle this?
The best way to handle your unique situation is to create your own project structure the way you need it to be. Create a parent project (main or standard) and then add phases to it. When done creating the structure you want, save the whole project structure as a project template from the detail view of the parent/main project (Actions > Save as Template). You can then reuse this template for all your future similar projects.