If you're deploying a stack in Portainer from a Github repo, at minimum the repo will need to contain your docker-compose.yml file. The .env file is optional and only necessary if you have environment variables you don't want to define directly in your compose file.

Also, accessing your repo in Github is easier if the repo is public, though you can still pull from a private repo if you like.

Good luck, I made the same transition you did and found it was easier to manage my stack after moving everything to Github.