Thanks for the quick reply so I assume you setup an IIS site called mail.domainname.com created the cert and then stored the cer file to use in smartermail configuration later on.
Currently with my setup I have webmail.domain.com and mail.domain.com on the same IP Address for IMAP/POP/Webmail etc I also have every single domain on the system setup with a webmail DNS Record pointing to the same IP which IIS Listens on.
So if I am right in thinking I need to the following:
1) Set the current IIS Site on the existing IP Address to answer to the host header mail.domainname.com + * & Install Cert in IIS
2) Create a new IIS Site called webmail.domainname.com with a new IP & Install cert in IIS
3) Configure Smartermail to use the cer for IMAP / POP3 / SMTP from above
I guess then customers who use webmail.theirdomain.com will go to the site in step2 and if they choose to use https there they would get a warning about invalid SSL Cert for domain in use.
It's all getting kind of confusing, just ordered by certs from servertastic though :)