I thought the sources for the 2nd zone were any that are hooked to the 990 (tuner,cd, dvd, turntable) and that when you called the 2nd zone into action you are simply choosing one of those inputs. I guess I don't follow your explaination of the 2nd set of analog cables.
The second zone is purely analog - if you're CD player is connected with a digital cable, the second zone won't have access to it. Obviously, this isn't an issue for some sources (tuner, turntable), but there are other sources that you wouldn't normally connect with analog cables.