The 'my domain' group just defaults to the domain you're on (where the Protect console is).
However, you can create a new machine group and list multiple domains for it to discover.
As long as the domains are trusted like you say they are and you provide proper credentials the scan and deployments should be able to run from a group like this.
Another option if you want to get more granular is to go to the 'Organization Unit' tab and browse active directory.
I hope that helps!
Ok thanks for the reply. Oddly, the first way does not work (via entire domain name) but the second way does (via AD OU). I think this will work though so thanks!