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:
*.mydomain.edu
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...