This has now been implemented: https://www.prisma.io/blog/organize-your-prisma-schema-with-multi-file-support

Like you correctly did before, you need to place every prisma file in prisma/schema.

In prisma/schema/schema.prisma you might want to update output so that the files are still created in the root of your project and not in prisma/:

output = "../generated/prisma" -> "../../generated/prisma"

Then, in the root of your project, create a file named prisma.config.ts:

import { defineConfig } from "prisma/config";

export default defineConfig({
  schema: "./prisma"
});

If you use a config file though, environment variables are not loaded automatically anymore, so, if you use them, you need to load them yourself by installing the package dotenv and adding this in the first line of prisma.config.ts:

import "dotenv/config";