The webserver uses the TLS certificate and corresponding private key for encrypting the connections. Therefore, the webserver needs to know where to find the certificate & private key. This has to be configured in the webserver.
From the text you’ve given us, you only ran certbot-auto with the certonly subcommand. This will only get you a certificate. But your webserver doesn’t have a crystal ball. The webserver doesn’t know what you want, until you tell it so. So you’ll have to configure your webserver properly for TLS and say where to find the certificate and private key.
If this doesn’t make any sense, you’d probably need to read a lot more about webservers and TLS in general and in my opinion you should leave this stuff to someone with more affinity/knowledge about this things.