Domain Aliases are a feature that was just added in today's release, so if you didn't update in the last hours you would not see it. That said, unless you're using a domain alias, you don't need to worry about that section.
Domain alias would be if you have realdomain.com and otherdomain.com and you want to provide API credentials for otherdomain.com even though you're getting certificates for realdomain.com (thus Cert Warden doesn't have credentials for realdomain.com but can get certificates for it).
Your provider should be for your domain [domain].net or wildcard * if you want. The token/credentials you specify on the provider need to be able to create and delete DNS records on [domain].net. If you manually created CNAME records in your DNS provider's console, remove them, they aren't needed.
What is your certificate Subject? Do you have any Subject Alternate Names ?
