Hi Daniel,
Are you asking if you can access the map service located in the Amazon EC2 AGS server from your Portal?
If this is the question, then yes you can. The external map services will act as any ESRI basemap. However for that work you need to allow the URL to pass through your firewall.
For use AD authentication on your map services you will need to setup a AD on your Amazon server and configure the connection between your company and this server (e.g.: site to site VPN).