If deploying through EE then use EnvironmentStack.template.json as well as optionally as well as upload sources.zip, cloud9-ide-instance.template.yaml and the functions folder to S3 and update the paths to indicate the path for the artifacts.
There is also EnvironmentStack-boostrap.template.json which is that but also runs bootstrap.sh on the Cloud9 to try to help set that up with the prerequiste steps for eksworkshop.com. The problem is that I can't see how to turn off AWS Managed Credentials and so you still need to flip that off before you can run some of them like aws eks update-kubeconfig etc.
If not deploying through EE then use EnvironmentStack-notEE.template.json - which doesn't set the team OwnerArn instead using the Role of whomever deploys the whole Stack but is otherwise the same.