It is easier to think of the SSL termination in legs.

1. Client to Cloudflare; if you’re behind orange cloud, you get this for free, don’t turn orange cloud off unless you want to have direct exposure.
2. Cloudflare to your sever; use their origin cert, this is easiest and secure. You can even get one made specific so your subdomains, or wildcard of your subdomain. Unless you have specific compliance needs, you shouldn’t need to turn this off, and you don’t need to roll your own cert.
3. Your reverse proxy to your apps; honestly, it’s already on your machine, you can do self signed cert if it really bothers you, but at the end of the day, probably not worth the hassle.

If, however, you want to directly expose your service without orange cloud (running a game server on the same subdomain for example), then you’d disable the orange cloud and do Let’s Encrypt or deploy your own certificate on your reverse proxy.