Custom database with Breeze

Loving Breeze as a starter kit, but curious how to deploy it on top of a custom made DB, such as one I would make in an ERD tool like Workbench. The keys and indexes have all been defined there, but having a Users table there might conflict with the users table of Breeze etc. Is there a canonical/easy way to merge them, or should I just reverse engineer Breeze tables, import them into my model, and re-export the model? Seems clunky if so.