I guess after I set SSL_KEY in secrets, in my app i need a function to put the SSL_KEY into a file and place the file in the root? how you accomplish this?
I don’t think you need to save it to a file in order to use it.
You could directly read the env variable in your app code and use it from there.
Steps 2 & 3 from Use Cloudflare Certs to FlyIO - #8 by ignoramous shows you how.
Or the SSL_KEY env will be automatically detected by fly.io as cert key? and I do not need to do anything from my side?
I’m afraid you have to handle TLS in your app 
Fly won’t auto-detect that env as a cert and do anything.