Bah, I leave for a few months and everybody stops thinking out of the box
I sorta did this by creating a 'ghost zone', AKA one of the unpowered zones, and having CQC monitor the keypad and route the command to the child zones. It's not independent control, they were both set to the same volume/power/source, but this way I could use 2 different amps for those 2 zones.
If you really want to do independent control, it's pretty easy. Use the keypad to put CQC on 'alert' that you're sending a command for zone <x>, then putting in the command. IE, let's pretend your zones are Z5 & Z6. Typing in 555-enter on the keypad will tell CQC that the next command on that keypad should be routed to Z5. Set a global variable called 'next-zone-command'. Once it sees 555-enter, it'll set the next-zone-command to 5. Once the next command is processed, clear out next-zone-command.
Obviously you don't have to do 555-enter, you could do any keycombo that you think is simple to remember.
I would think the whole thing would take less than 30 minutes to setup.