1. I think it depends on YOUR best time of day. When is your energy highest? I'm a total obnoxious morning person. My energy peaks and diminishes by 10:00 AM. For me, working out at 5:30 AM is awesome and if I workout in the afternoon I don't work nearly as hard. My girlfriend gets her best workouts in in the afternoon and would be sleep walking through 5:30 AM workouts.
2. I don't think twice a day is too much if you can fit it in and if it doesn't feel like too much. I think movement throughout the day is awesome. I get a good solid formal workout in during the morning, then I do something active in the afternoon, usually with the kids. This might be biking, walking, playing at the park, swimming, going to the amusement park, that kind of thing. Then in the evening, I'll often walk after dinner. But my formal no-excuses exercise I MUST get it is that time in the morning.
3. I think three is a myth, but I have no idea. I do go to be early and I do wake up early, but again...I'm the biggest morning person I know.
But I was also a morning person at 235 pounds and my metabolism wasn't really working for me then.