Eskos You're going to have to be a little more specific about the goal you're trying to achieve.
Note that the only requirement ITFlow has is that you "use SSL" (and that can be bypassed, not that we recommend that for production use). Setup of SSL Certs is purely beyond the scope of the web-app (but is provided in the setup script to make life easier).
Generally speaking, to make SSL work you either need to buy a certificate or get a free cert from somewhere like Let's Encrypt (usually via Certbot). You may need to validate ownership of your domain, often by adding a TXT record, but that's about it.
In the case of normal Cloudflare proxied traffic, you can use a valid SSL from a trusted CA, or generate an Origin CA that is only valid for Cloudflare to use when you proxy traffic via them (and they'll automatically generate the SSL for the user facing traffic). Again, I'm not familiar with the new tunnel software they now offer.