I would create the Project first, then go to the Deliverable/Milestone app and create the corresponding Deliverables/Milestones. I would use this pack of apps for this use case: https://podio.com/store/pack/1250-.
Have you seen the app reference article as well? It's here: https://help.podio.com/entries/21683251-app-references.
Hope that helps!
/Gustav - Podio