For now I have put my manual certificates back in place as I couldn't let it be down any longer.  Is just my home test server, but still, there are people using it.

As the system administrator, you can specify the storage location for the certificates in Webmail under Settings > SSL Certificates in the Options section. In addition to the storage path, you should also set a password to protect the certificates. You should store the password securely in a password manager.

Then configure your IIS server to access this certificate pool. There are many instructions for this on the Internet.

We also use HTTP-01 for domain verification so port 80 needs to respond for the cert to generate. SmarterMail should log any errors it is hung up on in the Certificates logs under: Manage > Troubleshooting > View Logs. Be sure to set the Certificates logs to Detailed to ensure more than errors are captured. Usually these only take a few minutes to generate when there are no hiccups.