The Let's Encrypt certificates manager allows you to install a Let's Encrypt certificate for mbox.your_domain.com - this is the location of your Webmail program.
To enable the certificate for your Webmail, you simply need to locate the mbox.your_domain.com hostname in the list of domains/subdomains in the Let's Encrypt certificates manager, check the box in front of it, and use the "Enable" button. If you have parked domains on your account and you use any of them to access your Webmail program (eg. mbox.parked_domain.com), you need to enable a certificate for each domain. If you enable a certificate for your * (wildcard) subdomain, it will be effective for your mbox subdomain as well.