Just throwing my 2 cents worth in because we also have 2 domains, but segmented networks with the exception of FOG talking over both networks. But that shouldn’t matter for this.
I have set up my primary domain information in FOG as a default. I then created Locations (Using the Location plugin) and host groups for each remote location. I then placed the machines into each of their respective host groups and applying the specifics there.
Once you have the machines you want on one domain placed into the host group for your Old domain, you can apply the AD information to that group allowing the Host that needs to remain on your Old domain to re-join it. You can do the same for the New domain as well.
Simply put: Create 2 Host Groups. “Old_Domain” and “New_Domain”. Place the hosts you want to keep on the old domain in the “Old_Domain” group and apply the AD information to that group. Then Place the hosts you want to be on the New Domain in the “New_Domain” group and apply the AD information to that group. Your hosts will stay on the domain you specified to each group.