For each domain you add, it will try to resolve autodiscover.ADDED_MAIL_DOMAIN and autoconfig.ADDED_MAIL_DOMAIN to your servers IPv4 address. If it succeeds, these names will be added as SANs to the certificate request.
You can skip the IP verification by adding SKIP_IP_CHECK=y to mailcow.conf (no quotes). Be warned that a misconfiguration will get you ratelimited by Let's Encrypt! This is primarily useful for multi-IP setups where the IP check would return the incorrect source IP. Due to using dynamic IPs for acme-mailcow, source NAT is not consistent over restarts.
For every domain you remove, the certificate will be moved and a new certificate will be requested. It is not possible to keep domains in a certificate, when we are not able validate the challenge for those.
To use your own certificates, just save the combined certificate (containing the certificate and intermediate CA/CA if any) to `data/assets/ssl/cert.pem` and the corresponding key to `data/assets/ssl/key.pem`.