FOG currently supports 1 default AD to join by default, and that information can be auto populated when you specify a host should auto join the domain after imaging.
You can however put the computers into a FOG group for each sub domain, and then use the group settings to specify the domain information to use when joined the subdomain.
I think the process would be to get them all registered with FOG, put them into a group, and then specify the AD option for the group. Those hosts should auto join the sub-domain you specified rather than the default domain.
I know this isn’t exactly what you’re asking for, but it’s how you can do it with the current version of FOG (0.32).