Yes, the architecture looks like you’ve described above. There is a Prisma GraphQL application that acts as a thin layer over your database. That API provides CRUD-based query and mutation capabilities. This application can, but doesn’t has to, be deployed on Graphcool servers. You can deploy it on a separate cloud provider as well (e.g. Digital Ocean). The CRUD functionality gets scaffolded from your data model.
The second application is the actual front-facing GraphQL API that would hold your business logic and uses Prisma for manipulating / reading your data.