My previous post was more a diagnosis of the problem than a solution. Your idea is worth a try, but I fear the trigger 2 signal will cut off when the main zone gets shut down. I actually wonder about some alternate method of triggering that stereo amp (something separate from the 990's triggers, assuming that the triggers really are tied to the main zone status).

Here's another idea to try: does trigger 1 come on when you turn on the second zone? I don't recall if it does or not, but if it does you could switch your trigger 1 and trigger 2 cables and set all of your inputs to engage trigger 2. In that scenario, having the main zone off would leave your EQ's, crossovers, and multichannel amp(s) off and trigger 1 would engage when the second zone was active. This only works if trigger 1 fires up when the second zone is on, though, and I don't know if that is the case or not.