There is a wire going to the antenna (I'm not in the car right now, but I think it's an orange wire). Whenever the head unit is turned on, there is a 12v signal going to the antenna motor - that's the one you want to control manually.
You have to cut that wire, insert a switch between the two ends, and voila: you have manual control. Whenever you need the antenna, turn the head unit on, then your switch, and the antenna will go up. Turn either one off, and the antenna goes down. If you leave the switch off during CD playback, it will stay down.
That's somewhere on my "to-do" list this summer.. I need 48-hours days!!