When several sites are hosted on the same server, it can be useful to get a single certificate that covers all (or at least several) of those sites' domains.
Whenever you run
certbot certonly, you'll get a single certificate. If you want that new certificate to cover several domains, all of those domains should be listed with
-d parameters. If you want them instead to be covered by separate certificates, you'll need to run
certbot certonly several times.
I'm not using your terms "URL" or "website" because the domain is only one part of the web site. The certificate directly covers domain names, not web sites (for example, in https://www.example.com/foo and https://www.example.com/bar, the domain name is
To learn more about how web servers can host multiple HTTPS sites on the same IP address, you should read about server name indication (SNI) and subject alternative names (SAN). The
-d parameters to a single Certbot command provide domain names that will be listed as SANs in the resulting certificate (up to a maximum of 100 names).