So we got our CA-signed SSL Certifcate for use with the web-adapter, however the certificate is made out to <mydomian.edu> but when i go to but the actual domain is <ad.mydomain.edu> is this going to be a problem in getting Portal to come up as secure?
You should be fine.
If you install that certificate and then were to look into it, you'd see that it covers:
So ad.mydomain.edu or site2.mydomain.edu or site1.subsite.mydomain.edu are all going to be covered by that domain certificate.
That's the beauty of the domain certificate.
You could also claim that's the weakness of a domain cert since it can cover anything created inside the domain and we can't control what others create. Keys to the kingdom thing...