SSL certificate and Alias/CNAME setup

I have been attempting to set up Password Manager Pro with an SSL certificate that will work with an Alias/CNAME.  I have followed the documentation on how to create the keystore and request file using the java commands and am able to create the certificate however if I attempt to access the site via the Alias/CNAME I always get the message about there being a problem with the website’s certificate and need to click continue to proceed to the website.  If I use the actual name of the server hosting the Password Manager Pro site it work correctly (no certificate error message to click continue on).  Please advise what I need to do in order to make the certificate work with an Alias/CNAME.