I have a custom dns entry mapped to my traffic manager setup via CNAME record. I also have traffic manager pointing to my azure website endpoint and I have a wildcard cert
Have you seen this blog post by Scott Hanselman? http://www.hanselman.com/blog/CloudPowerHowToScaleAzureWebsitesGloballyWithTrafficManager.aspx
You don't upload the certificate to traffic manager. You upload it and set it up for each of the individual sites that the traffic manager will route your customers to