Do these in Exchange command shell, replacing all site data as indicated (US is the short geographical form):
$Data = New-ExchangeCertificate -GenerateRequest -SubjectName "c=US, o=Organization Name, cn=fqdn.organization.com" -DomainName organization.com, secondarydomain.com -PrivateKeyExportable $true Set-Content -path "C:\Docs\MyCertRequest.req" -Value $Data
Then get the thumbprint for the certificate request created above:
get-exchangecertificate
and paste it into this (replacing the thumbprint via copy/paste):
get-exchangecertificate -thumbprint asdfdefghijklmnopqrstuvwxyz | new-exchangecertificate
and then, most likely (again replacing the thumbprint via copy/paste):
enable-exchangecertificate -thumbprint asdfdefghijklmnopqrstuvwxyz -Services POP,IMAP,SMTP,IIS